Structured Review

Roche qrt pcr analysis
ANG regulates primitive hematopoietic cell properties through PLXNB2 (A) Quantification of HSPC cell cycle status of Mx1-specific Plxnb2 −/− mice (n=9). (B) Serial re-plating colony assay of whole BM cells (n=2). ANG was added at each re-plating. (C) Experimental schema of transplant using Mx1-specific Plxnb2 −/− whole BM as donors. (D) Multi-lineage donor cell chimerism after competitive transplant of Mx1-specific Plxnb2 −/− donors (n=5). (E-F) ANG (0.3 μg/ml) regulates LT-HSC proliferation (E, n=3) and pro-self-renewal transcripts (F, n=3) from WT but not from Mx1-specific Plxnb2 −/− mice. (G) Quantification of HSPC cell cycle status of mAb17-treated WT or Ang −/− mice (n=6). (H-I) Cell density on day 7 (H, n=3) and <t>qRT-PCR</t> analysis of pro-self-renewal transcripts (I, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml ANG, 50 μg/ml mAb17, or both. (J-K) Cell density on day 7 (J, n=3) or qRT-PCR analysis of pro-self-renewal transcripts (K, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml Sema4C, 50 μg/ml mAb17, or both. (L) Experimental schema of transplant using sorted WT LT-HSC that had been cultured with 0.3 μg/ml ANG, 50 μg/ml mAb17, or both for 7 days. (M) Multi-lineage donor cell chimerism after competitive transplant of ANG and/or mAb17-treated WT LT-HSC donors (n=6). .
Qrt Pcr Analysis, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 226 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/qrt pcr analysis/product/Roche
Average 93 stars, based on 226 article reviews
Price from $9.99 to $1999.99
qrt pcr analysis - by Bioz Stars, 2020-02
93/100 stars

Images

1) Product Images from "Plexin-B2 mediates physiologic and pathologic functions of angiogenin"

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin

Journal: Cell

doi: 10.1016/j.cell.2017.10.005

ANG regulates primitive hematopoietic cell properties through PLXNB2 (A) Quantification of HSPC cell cycle status of Mx1-specific Plxnb2 −/− mice (n=9). (B) Serial re-plating colony assay of whole BM cells (n=2). ANG was added at each re-plating. (C) Experimental schema of transplant using Mx1-specific Plxnb2 −/− whole BM as donors. (D) Multi-lineage donor cell chimerism after competitive transplant of Mx1-specific Plxnb2 −/− donors (n=5). (E-F) ANG (0.3 μg/ml) regulates LT-HSC proliferation (E, n=3) and pro-self-renewal transcripts (F, n=3) from WT but not from Mx1-specific Plxnb2 −/− mice. (G) Quantification of HSPC cell cycle status of mAb17-treated WT or Ang −/− mice (n=6). (H-I) Cell density on day 7 (H, n=3) and qRT-PCR analysis of pro-self-renewal transcripts (I, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml ANG, 50 μg/ml mAb17, or both. (J-K) Cell density on day 7 (J, n=3) or qRT-PCR analysis of pro-self-renewal transcripts (K, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml Sema4C, 50 μg/ml mAb17, or both. (L) Experimental schema of transplant using sorted WT LT-HSC that had been cultured with 0.3 μg/ml ANG, 50 μg/ml mAb17, or both for 7 days. (M) Multi-lineage donor cell chimerism after competitive transplant of ANG and/or mAb17-treated WT LT-HSC donors (n=6). .
Figure Legend Snippet: ANG regulates primitive hematopoietic cell properties through PLXNB2 (A) Quantification of HSPC cell cycle status of Mx1-specific Plxnb2 −/− mice (n=9). (B) Serial re-plating colony assay of whole BM cells (n=2). ANG was added at each re-plating. (C) Experimental schema of transplant using Mx1-specific Plxnb2 −/− whole BM as donors. (D) Multi-lineage donor cell chimerism after competitive transplant of Mx1-specific Plxnb2 −/− donors (n=5). (E-F) ANG (0.3 μg/ml) regulates LT-HSC proliferation (E, n=3) and pro-self-renewal transcripts (F, n=3) from WT but not from Mx1-specific Plxnb2 −/− mice. (G) Quantification of HSPC cell cycle status of mAb17-treated WT or Ang −/− mice (n=6). (H-I) Cell density on day 7 (H, n=3) and qRT-PCR analysis of pro-self-renewal transcripts (I, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml ANG, 50 μg/ml mAb17, or both. (J-K) Cell density on day 7 (J, n=3) or qRT-PCR analysis of pro-self-renewal transcripts (K, n=3) from sorted WT or Ang −/− LT-HSC cultured in the presence of 0.3 μg/ml Sema4C, 50 μg/ml mAb17, or both. (L) Experimental schema of transplant using sorted WT LT-HSC that had been cultured with 0.3 μg/ml ANG, 50 μg/ml mAb17, or both for 7 days. (M) Multi-lineage donor cell chimerism after competitive transplant of ANG and/or mAb17-treated WT LT-HSC donors (n=6). .

Techniques Used: Mouse Assay, Colony Assay, Quantitative RT-PCR, Cell Culture

Cell type-specific regulation of protein synthesis by ANG-PLXNB2 (A-B) Quantification of MyePro cell cycle status of WT and Mx1-specific Plxnb2 −/− (A, n=9) and mAb17-treated WT or Ang −/− mice (B, n=6). (C-D) OP-Puro incorporation following 2 h ANG treatment of WT or Mx1-specific Plxnb2 −/− HSPC and MyePro for cells in all phases (C, n=4) or in G0/G1 phase (D, n=4). (E) qRT-PCR analysis of rRNA following 2 h ANG treatment of WT or Mx1-specific Plxnb2 −/− HSPC and MyePro (n=3). (F-G) Small RNA production in Mx1-specific Plxnb2 −/− HSPC (F, n=2) or WT HSPC treated with 0.3 μg/ml ANG, 50 μg/ml mAb17, or both (G, n=2).
Figure Legend Snippet: Cell type-specific regulation of protein synthesis by ANG-PLXNB2 (A-B) Quantification of MyePro cell cycle status of WT and Mx1-specific Plxnb2 −/− (A, n=9) and mAb17-treated WT or Ang −/− mice (B, n=6). (C-D) OP-Puro incorporation following 2 h ANG treatment of WT or Mx1-specific Plxnb2 −/− HSPC and MyePro for cells in all phases (C, n=4) or in G0/G1 phase (D, n=4). (E) qRT-PCR analysis of rRNA following 2 h ANG treatment of WT or Mx1-specific Plxnb2 −/− HSPC and MyePro (n=3). (F-G) Small RNA production in Mx1-specific Plxnb2 −/− HSPC (F, n=2) or WT HSPC treated with 0.3 μg/ml ANG, 50 μg/ml mAb17, or both (G, n=2).

Techniques Used: Mouse Assay, Quantitative RT-PCR

2) Product Images from "Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells"

Article Title: Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0168875

Relative expression values and heatmap figure of MAPK signaling pathway-related genes. (A) Relative expression values obtained from qRT-PCR analysis for each gene are shown on the y-axis in arbitrary units. The data were obtained from 12 independent PCOS patients. Each patient provided both cell types, CC and MGC. The data are presented as mean ± SEM. Asterisk (*) indicates a significant difference (p
Figure Legend Snippet: Relative expression values and heatmap figure of MAPK signaling pathway-related genes. (A) Relative expression values obtained from qRT-PCR analysis for each gene are shown on the y-axis in arbitrary units. The data were obtained from 12 independent PCOS patients. Each patient provided both cell types, CC and MGC. The data are presented as mean ± SEM. Asterisk (*) indicates a significant difference (p

Techniques Used: Expressing, Quantitative RT-PCR

Relative expression of candidate genes (FZD3, INSR, PTPRC, RUNX2 and JUNB) obtained from qRT-PCR analysis. The validation study was performed with 12 independent patients who provided two somatic cell types: CC and MGC. Relative expression values for each gene is shown on the y-axis in arbitrary units. The data are presented as mean ± SEM. Asterisk (*) indicates a significant difference (p
Figure Legend Snippet: Relative expression of candidate genes (FZD3, INSR, PTPRC, RUNX2 and JUNB) obtained from qRT-PCR analysis. The validation study was performed with 12 independent patients who provided two somatic cell types: CC and MGC. Relative expression values for each gene is shown on the y-axis in arbitrary units. The data are presented as mean ± SEM. Asterisk (*) indicates a significant difference (p

Techniques Used: Expressing, Quantitative RT-PCR

3) Product Images from "Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects"

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects

Journal: Brazilian Journal of Medical and Biological Research

doi: 10.1590/S0100-879X2012007500123

HNP 1-3 and LL-37 mRNA expression in peripheral neutrophils from periodontitis and healthy subjects. Neutrophils were isolated from peripheral blood and analyzed by flow cytometry, showing more than 94% purity according to side scatter (SSC) vs forward scatter (FSC) parameters ( A ). Neutrophils were incubated for 6 and 12 h with culture medium only or with medium containing Aa -LPS (100 ng/mL), Pg -LPS (100 ng/mL) or Ec -LPS (100 ng/mL). The relative mRNA expression of HNP 1-3 ( B ) and LL-37 ( C ) in neutrophils was assessed by qRT-PCR. Data are reported as means ± SD for N = 6 in each group. Aa -LPS = Aggregatibacter actinomycetemcomitans -lipopolysaccharide; Pg -LPS = Porphyromonas gingivalis -LPS; Ec -LPS = Escherichia coli -LPS. * P ≤ 0.05, periodontitis compared to healthy subjects (Student t -test).
Figure Legend Snippet: HNP 1-3 and LL-37 mRNA expression in peripheral neutrophils from periodontitis and healthy subjects. Neutrophils were isolated from peripheral blood and analyzed by flow cytometry, showing more than 94% purity according to side scatter (SSC) vs forward scatter (FSC) parameters ( A ). Neutrophils were incubated for 6 and 12 h with culture medium only or with medium containing Aa -LPS (100 ng/mL), Pg -LPS (100 ng/mL) or Ec -LPS (100 ng/mL). The relative mRNA expression of HNP 1-3 ( B ) and LL-37 ( C ) in neutrophils was assessed by qRT-PCR. Data are reported as means ± SD for N = 6 in each group. Aa -LPS = Aggregatibacter actinomycetemcomitans -lipopolysaccharide; Pg -LPS = Porphyromonas gingivalis -LPS; Ec -LPS = Escherichia coli -LPS. * P ≤ 0.05, periodontitis compared to healthy subjects (Student t -test).

Techniques Used: Expressing, Isolation, Flow Cytometry, Cytometry, Incubation, Quantitative RT-PCR

4) Product Images from "Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing"

Article Title: Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms20020441

( A ) Heat maps of the blue light signaling networks in up- and downregulated genes. ( B ) qRT-PCR analysis of candidate genes involved in the blue light stress response. From red to blue corresponds to a decreasing value of FPKM. CRY1, cryptochrome 1; CRY2, cryptochrome; COP1, constitutive photomorphogenic 1; HY5, long hypocotyl 5; MYC2, basic helix-loop-helix transcription factor; PIF, phytochrome-interacting factor; SPA1, phytochrome A suppressor 1; CIB1, cryptochrome-interacting basic-helix-loop-helix 1; CO, constants.
Figure Legend Snippet: ( A ) Heat maps of the blue light signaling networks in up- and downregulated genes. ( B ) qRT-PCR analysis of candidate genes involved in the blue light stress response. From red to blue corresponds to a decreasing value of FPKM. CRY1, cryptochrome 1; CRY2, cryptochrome; COP1, constitutive photomorphogenic 1; HY5, long hypocotyl 5; MYC2, basic helix-loop-helix transcription factor; PIF, phytochrome-interacting factor; SPA1, phytochrome A suppressor 1; CIB1, cryptochrome-interacting basic-helix-loop-helix 1; CO, constants.

Techniques Used: Quantitative RT-PCR

5) Product Images from "JunB regulates homeostasis and suppressive functions of effector regulatory T cells"

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells

Journal: Nature Communications

doi: 10.1038/s41467-018-07735-4

Expression of JunB is upregulated in eTreg cells. a – d Flow cytometry analysis of JunB in Foxp3 + (Treg) or Foxp3 − (Tconv) cells isolated from spleen a and lung b , Treg cells bearing CD62L hi CD44 lo phenotypes (cTreg) or CD62L lo phenotypes (eTreg) c , and ICOS + or ICOS − eTreg cells d isolated from spleen of wild-type C57BL/6 mice (7–10-week-old). Cd4 cre Junb fl/fl mice were used as negative controls. e CD62L hi CD44 lo cTreg and CD62L lo eTreg cells were sorted by FACS, and Junb mRNA expression was analyzed by qRT-PCR. a – e Error bars indicate s.d. ( n = 4). * P
Figure Legend Snippet: Expression of JunB is upregulated in eTreg cells. a – d Flow cytometry analysis of JunB in Foxp3 + (Treg) or Foxp3 − (Tconv) cells isolated from spleen a and lung b , Treg cells bearing CD62L hi CD44 lo phenotypes (cTreg) or CD62L lo phenotypes (eTreg) c , and ICOS + or ICOS − eTreg cells d isolated from spleen of wild-type C57BL/6 mice (7–10-week-old). Cd4 cre Junb fl/fl mice were used as negative controls. e CD62L hi CD44 lo cTreg and CD62L lo eTreg cells were sorted by FACS, and Junb mRNA expression was analyzed by qRT-PCR. a – e Error bars indicate s.d. ( n = 4). * P

Techniques Used: Expressing, Flow Cytometry, Cytometry, Isolation, Mouse Assay, FACS, Quantitative RT-PCR

6) Product Images from "Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis"

Article Title: Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis

Journal: Human Vaccines & Immunotherapeutics

doi: 10.4161/hv.26969

Figure 3. mRNA levels of IFN-γ, IL-10, TNF-α, and iNOS in the lung of different vaccinated mice detected by qRT-PCR (n = 5). Tested cDNAs were normalized to the endogenous RNA levels of the internal control GAPDH. The fold increase of gene expression in vaccinated group was calculated using 2 −ΔΔCT method. The results were shown as mean ± SD.
Figure Legend Snippet: Figure 3. mRNA levels of IFN-γ, IL-10, TNF-α, and iNOS in the lung of different vaccinated mice detected by qRT-PCR (n = 5). Tested cDNAs were normalized to the endogenous RNA levels of the internal control GAPDH. The fold increase of gene expression in vaccinated group was calculated using 2 −ΔΔCT method. The results were shown as mean ± SD.

Techniques Used: Mouse Assay, Quantitative RT-PCR, Expressing

7) Product Images from "DDX39B promotes translation through regulation of pre-ribosomal RNA levels"

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels

Journal: RNA Biology

doi: 10.1080/15476286.2018.1517011

DDX39B regulates the stability and transcription of pre-ribosomal RNA. (A) DDX39B perturbation affects the stability of pre-ribosomal RNA. HEK293 cells were transfected with control or siDDX39B-1 or pEGFP-C1 vector or pEGFP-DDX39B. After 48 hours of transfection, the cells were harvested at the indicated time points after the addition of actinomycin D. The levels of 47S rRNA were then quantified by qRT-PCR. The 47S rRNA levels were normalized to GAPDH expression and are presented relative to the 0 min time point sample. Data are represented as mean of three independent experiments. The error bars represent standard deviations. (B) DDX39B is required for efficient synthesis of pre-ribosomal rRNA. The control or DDX39B knock down HeLa cells were pulse labelled with 5-fluorouridine (5-FUrd) and immunostained with BrdU antibody (left panel). DNA was stained with DAPI (middle panel). The right panel shows the merge of fluorescent images. The graph at the bottom of the panel represents the quantification of fluorescence signals in 55 cells of each group. The quantification of fluorescence signals was done by using ImageJ software. Statistical significance was assessed using nonparametric Wilcoxon rank-sum test. P-Values are depicted. (C) DDX39B is recruited to the promoter and regulatory regions of rDNA. The chromatin was prepared from HEK293 cells and fragmented (upper panel gel image). Immunoprecipitation was performed using rabbit IgG antibody or DDX39B antibody. The immunoprecipitated DNA was investigated for the enrichment of promoter and regulatory regions of rDNA and two random control regions (YY2 and CALML3) by using qRT-PCR. The primer binding locations in the rDNA locus are indicated in the schema (above the graph). Data are shown relative to input and the values represent the mean of three independent experiments, with the error bars depicting standard deviations.
Figure Legend Snippet: DDX39B regulates the stability and transcription of pre-ribosomal RNA. (A) DDX39B perturbation affects the stability of pre-ribosomal RNA. HEK293 cells were transfected with control or siDDX39B-1 or pEGFP-C1 vector or pEGFP-DDX39B. After 48 hours of transfection, the cells were harvested at the indicated time points after the addition of actinomycin D. The levels of 47S rRNA were then quantified by qRT-PCR. The 47S rRNA levels were normalized to GAPDH expression and are presented relative to the 0 min time point sample. Data are represented as mean of three independent experiments. The error bars represent standard deviations. (B) DDX39B is required for efficient synthesis of pre-ribosomal rRNA. The control or DDX39B knock down HeLa cells were pulse labelled with 5-fluorouridine (5-FUrd) and immunostained with BrdU antibody (left panel). DNA was stained with DAPI (middle panel). The right panel shows the merge of fluorescent images. The graph at the bottom of the panel represents the quantification of fluorescence signals in 55 cells of each group. The quantification of fluorescence signals was done by using ImageJ software. Statistical significance was assessed using nonparametric Wilcoxon rank-sum test. P-Values are depicted. (C) DDX39B is recruited to the promoter and regulatory regions of rDNA. The chromatin was prepared from HEK293 cells and fragmented (upper panel gel image). Immunoprecipitation was performed using rabbit IgG antibody or DDX39B antibody. The immunoprecipitated DNA was investigated for the enrichment of promoter and regulatory regions of rDNA and two random control regions (YY2 and CALML3) by using qRT-PCR. The primer binding locations in the rDNA locus are indicated in the schema (above the graph). Data are shown relative to input and the values represent the mean of three independent experiments, with the error bars depicting standard deviations.

Techniques Used: Transfection, Plasmid Preparation, Quantitative RT-PCR, Expressing, Staining, Fluorescence, Software, Immunoprecipitation, Binding Assay

DDX39B regulates the levels of pre-ribosomal RNA. (A) Efficiency of siRNA mediated knockdown of DDX39B by qRT-PCR. HEK293 cells were treated with control siRNA or DDX39B siRNA-1 (siDDX39B-1) or DDX39B siRNA-2 (siDDX39B-2) and transcript levels of DDX39B were quantified using qRT-PCR. DDX39B transcripts levels were normalized to GAPDH expression and are presented relative to the control sample. Data are represented as mean of three independent experiments, with error bars representing standard deviation. Statistical significance was assessed by two tailed t-Test: paired two samples for means. ** represents P-value
Figure Legend Snippet: DDX39B regulates the levels of pre-ribosomal RNA. (A) Efficiency of siRNA mediated knockdown of DDX39B by qRT-PCR. HEK293 cells were treated with control siRNA or DDX39B siRNA-1 (siDDX39B-1) or DDX39B siRNA-2 (siDDX39B-2) and transcript levels of DDX39B were quantified using qRT-PCR. DDX39B transcripts levels were normalized to GAPDH expression and are presented relative to the control sample. Data are represented as mean of three independent experiments, with error bars representing standard deviation. Statistical significance was assessed by two tailed t-Test: paired two samples for means. ** represents P-value

Techniques Used: Quantitative RT-PCR, Expressing, Standard Deviation, Two Tailed Test

8) Product Images from "DDX39B promotes translation through regulation of pre-ribosomal RNA levels"

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels

Journal: RNA Biology

doi: 10.1080/15476286.2018.1517011

DDX39B regulates the stability and transcription of pre-ribosomal RNA. (A) DDX39B perturbation affects the stability of pre-ribosomal RNA. HEK293 cells were transfected with control or siDDX39B-1 or pEGFP-C1 vector or pEGFP-DDX39B. After 48 hours of transfection, the cells were harvested at the indicated time points after the addition of actinomycin D. The levels of 47S rRNA were then quantified by qRT-PCR. The 47S rRNA levels were normalized to GAPDH expression and are presented relative to the 0 min time point sample. Data are represented as mean of three independent experiments. The error bars represent standard deviations. (B) DDX39B is required for efficient synthesis of pre-ribosomal rRNA. The control or DDX39B knock down HeLa cells were pulse labelled with 5-fluorouridine (5-FUrd) and immunostained with BrdU antibody (left panel). DNA was stained with DAPI (middle panel). The right panel shows the merge of fluorescent images. The graph at the bottom of the panel represents the quantification of fluorescence signals in 55 cells of each group. The quantification of fluorescence signals was done by using ImageJ software. Statistical significance was assessed using nonparametric Wilcoxon rank-sum test. P-Values are depicted. (C) DDX39B is recruited to the promoter and regulatory regions of rDNA. The chromatin was prepared from HEK293 cells and fragmented (upper panel gel image). Immunoprecipitation was performed using rabbit IgG antibody or DDX39B antibody. The immunoprecipitated DNA was investigated for the enrichment of promoter and regulatory regions of rDNA and two random control regions (YY2 and CALML3) by using qRT-PCR. The primer binding locations in the rDNA locus are indicated in the schema (above the graph). Data are shown relative to input and the values represent the mean of three independent experiments, with the error bars depicting standard deviations.
Figure Legend Snippet: DDX39B regulates the stability and transcription of pre-ribosomal RNA. (A) DDX39B perturbation affects the stability of pre-ribosomal RNA. HEK293 cells were transfected with control or siDDX39B-1 or pEGFP-C1 vector or pEGFP-DDX39B. After 48 hours of transfection, the cells were harvested at the indicated time points after the addition of actinomycin D. The levels of 47S rRNA were then quantified by qRT-PCR. The 47S rRNA levels were normalized to GAPDH expression and are presented relative to the 0 min time point sample. Data are represented as mean of three independent experiments. The error bars represent standard deviations. (B) DDX39B is required for efficient synthesis of pre-ribosomal rRNA. The control or DDX39B knock down HeLa cells were pulse labelled with 5-fluorouridine (5-FUrd) and immunostained with BrdU antibody (left panel). DNA was stained with DAPI (middle panel). The right panel shows the merge of fluorescent images. The graph at the bottom of the panel represents the quantification of fluorescence signals in 55 cells of each group. The quantification of fluorescence signals was done by using ImageJ software. Statistical significance was assessed using nonparametric Wilcoxon rank-sum test. P-Values are depicted. (C) DDX39B is recruited to the promoter and regulatory regions of rDNA. The chromatin was prepared from HEK293 cells and fragmented (upper panel gel image). Immunoprecipitation was performed using rabbit IgG antibody or DDX39B antibody. The immunoprecipitated DNA was investigated for the enrichment of promoter and regulatory regions of rDNA and two random control regions (YY2 and CALML3) by using qRT-PCR. The primer binding locations in the rDNA locus are indicated in the schema (above the graph). Data are shown relative to input and the values represent the mean of three independent experiments, with the error bars depicting standard deviations.

Techniques Used: Transfection, Plasmid Preparation, Quantitative RT-PCR, Expressing, Staining, Fluorescence, Software, Immunoprecipitation, Binding Assay

DDX39B regulates the levels of pre-ribosomal RNA. (A) Efficiency of siRNA mediated knockdown of DDX39B by qRT-PCR. HEK293 cells were treated with control siRNA or DDX39B siRNA-1 (siDDX39B-1) or DDX39B siRNA-2 (siDDX39B-2) and transcript levels of DDX39B were quantified using qRT-PCR. DDX39B transcripts levels were normalized to GAPDH expression and are presented relative to the control sample. Data are represented as mean of three independent experiments, with error bars representing standard deviation. Statistical significance was assessed by two tailed t-Test: paired two samples for means. ** represents P-value
Figure Legend Snippet: DDX39B regulates the levels of pre-ribosomal RNA. (A) Efficiency of siRNA mediated knockdown of DDX39B by qRT-PCR. HEK293 cells were treated with control siRNA or DDX39B siRNA-1 (siDDX39B-1) or DDX39B siRNA-2 (siDDX39B-2) and transcript levels of DDX39B were quantified using qRT-PCR. DDX39B transcripts levels were normalized to GAPDH expression and are presented relative to the control sample. Data are represented as mean of three independent experiments, with error bars representing standard deviation. Statistical significance was assessed by two tailed t-Test: paired two samples for means. ** represents P-value

Techniques Used: Quantitative RT-PCR, Expressing, Standard Deviation, Two Tailed Test

9) Product Images from "Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]"

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]

Journal: 3 Biotech

doi: 10.1007/s13205-018-1553-z

Expression analysis of transformed soybean plants. a RT-PCR expression analysis of p68 gene in transformed soybean plants. Lane 1, non-transformed (NT) soybean plant RNA as a negative control; lanes 2, 4 and 6, transformed (T 1 ) soybean (S1, S12 and S15) plant RNA samples; lanes 3 and 5, failed to amplify p68 gene from transformed (T 1 ) soybean (S2 and S13) plant RNA samples. b qRT-PCR analysis to analyze the expression level of p68 gene in transformed soybean plants. Relative expression of three transgenic lines (S1, S12 and S15) and non-transformed (NT) soybean plant; data were analyzed according to the 2 − ΔΔCt method. Mean of three individual experiments with standard errors. Different letters denote significantly different values according to Duncan’s multiple range test (DMRT) at a 5% level
Figure Legend Snippet: Expression analysis of transformed soybean plants. a RT-PCR expression analysis of p68 gene in transformed soybean plants. Lane 1, non-transformed (NT) soybean plant RNA as a negative control; lanes 2, 4 and 6, transformed (T 1 ) soybean (S1, S12 and S15) plant RNA samples; lanes 3 and 5, failed to amplify p68 gene from transformed (T 1 ) soybean (S2 and S13) plant RNA samples. b qRT-PCR analysis to analyze the expression level of p68 gene in transformed soybean plants. Relative expression of three transgenic lines (S1, S12 and S15) and non-transformed (NT) soybean plant; data were analyzed according to the 2 − ΔΔCt method. Mean of three individual experiments with standard errors. Different letters denote significantly different values according to Duncan’s multiple range test (DMRT) at a 5% level

Techniques Used: Expressing, Transformation Assay, Reverse Transcription Polymerase Chain Reaction, Negative Control, Quantitative RT-PCR, Transgenic Assay

10) Product Images from "Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane"

Article Title: Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane

Journal: BMC Genomics

doi: 10.1186/s12864-017-4142-3

qRT-PCR analysis of seven sugarcane ScJAZ family genes in 4-month-old ROC22 plantlets after treatment with 25% PEG, 10 μM H 2 O 2 , 250 mM NaCl, 100 mM CuCl 2 , and 100 mM CaCl 2 . Data were normalized to the expression level of the GAPDH gene. All data points were expressed as the mean ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value
Figure Legend Snippet: qRT-PCR analysis of seven sugarcane ScJAZ family genes in 4-month-old ROC22 plantlets after treatment with 25% PEG, 10 μM H 2 O 2 , 250 mM NaCl, 100 mM CuCl 2 , and 100 mM CaCl 2 . Data were normalized to the expression level of the GAPDH gene. All data points were expressed as the mean ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value

Techniques Used: Quantitative RT-PCR, Expressing

Tissue-specific expression analysis of seven ScJAZ family genes in different 10-month-old ROC22 tissues by qRT-PCR. Data was normalized to the GAPDH expression level. All data points are the means ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value
Figure Legend Snippet: Tissue-specific expression analysis of seven ScJAZ family genes in different 10-month-old ROC22 tissues by qRT-PCR. Data was normalized to the GAPDH expression level. All data points are the means ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value

Techniques Used: Expressing, Quantitative RT-PCR

qRT-PCR analysis of seven sugarcane ScJAZ family genes in 4-month-old ROC22 plantlets after treatment with 5 mM SA, 100 μM MeJA and 100 μM ABA. Data was normalized to the GAPDH expression level. All data points were the means ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value
Figure Legend Snippet: qRT-PCR analysis of seven sugarcane ScJAZ family genes in 4-month-old ROC22 plantlets after treatment with 5 mM SA, 100 μM MeJA and 100 μM ABA. Data was normalized to the GAPDH expression level. All data points were the means ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value

Techniques Used: Quantitative RT-PCR, Expressing

Expression analysis of seven sugarcane ScJAZ family genes during sugarcane- Sporisorium scitamineum interaction by qRT-PCR. Data was normalized to the GAPDH expression level. All data points (with the deduction of their mocks) were expressed as the mean ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value
Figure Legend Snippet: Expression analysis of seven sugarcane ScJAZ family genes during sugarcane- Sporisorium scitamineum interaction by qRT-PCR. Data was normalized to the GAPDH expression level. All data points (with the deduction of their mocks) were expressed as the mean ± SE ( n = 3). Different lowercase letters indicate a significant difference, as determined by the Duncan’s new multiple range test ( p -value

Techniques Used: Expressing, Quantitative RT-PCR

11) Product Images from "RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides"

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1007109

Toll4 regulates Dorsal activation in response to WSSV infection in shrimp. (A) Silencing efficiency for Toll4 in hemocytes was detected by qRT-PCR. (B) Dorsal nuclear translocation in Toll4 silenced hemocytes at 6 h post WSSV infection. (b) Statistical analysis of co-localization of Dorsal and nucleus in hemocytes by WCIF ImageJ software. (C) The subcellular distribution of Dorsal in Toll4 silenced hemocytes was detected at 6 h post WSSV infection by western blotting. The GFP dsRNA treated hemocytes was used as a control. (D) Dorsal phosphorylation level (Ser342) in Toll4 dsRNA and GFP dsRNA treated hemocytes was probed by western blotting. (E) Cactus protein levels were detected by western blotting using prepared anti-Cactus specific antibody in Toll4 dsRNA and GFP dsRNA treated hemocytes at 6 h post WSSV infection. The dsRNA untreated and WSSV non-challenged hemocytes were used as control. (c, d, e) Statistical analysis of the Dorsal nuclear translocation proportion, Dorsal phosphorylation levels and Cactus protein levels in Toll4 dsRNA and GFP dsRNA treated hemocytes at 6 h post WSSV infection, respectively. All experiments were performed three times, and similar results were observed. All the data from b, c, d and e were analyzed statistically by student’s T test (** p
Figure Legend Snippet: Toll4 regulates Dorsal activation in response to WSSV infection in shrimp. (A) Silencing efficiency for Toll4 in hemocytes was detected by qRT-PCR. (B) Dorsal nuclear translocation in Toll4 silenced hemocytes at 6 h post WSSV infection. (b) Statistical analysis of co-localization of Dorsal and nucleus in hemocytes by WCIF ImageJ software. (C) The subcellular distribution of Dorsal in Toll4 silenced hemocytes was detected at 6 h post WSSV infection by western blotting. The GFP dsRNA treated hemocytes was used as a control. (D) Dorsal phosphorylation level (Ser342) in Toll4 dsRNA and GFP dsRNA treated hemocytes was probed by western blotting. (E) Cactus protein levels were detected by western blotting using prepared anti-Cactus specific antibody in Toll4 dsRNA and GFP dsRNA treated hemocytes at 6 h post WSSV infection. The dsRNA untreated and WSSV non-challenged hemocytes were used as control. (c, d, e) Statistical analysis of the Dorsal nuclear translocation proportion, Dorsal phosphorylation levels and Cactus protein levels in Toll4 dsRNA and GFP dsRNA treated hemocytes at 6 h post WSSV infection, respectively. All experiments were performed three times, and similar results were observed. All the data from b, c, d and e were analyzed statistically by student’s T test (** p

Techniques Used: Activation Assay, Infection, Quantitative RT-PCR, Translocation Assay, Software, Western Blot

The function of Toll4-Dorsal cascade regulated AMPs in WSSV infection. (A) Effective knockdown for ALF1-4 and LYZ1-4 in hemocytes by dsRNA was confirmed by qRT-PCR. (B-F) Silencing of AMPs enhanced WSSV infection in shrimp. WSSV was inoculated at 48 h post each AMP silencing. The viral loads in gills were assessed at 24 h (B), 48 h (C), 72 h (D), 96 h (E) and 120 h (F) post-infection via absolute qPCR. (G-H) Survival of WSSV challenged AMP-silenced shrimp and GFP dsRNA treated shrimp. All experiments were performed three times, and similar results were obtained. All the data from B, C, D, E and F were analyzed statistically by student’s T test (NS, not significant; * p
Figure Legend Snippet: The function of Toll4-Dorsal cascade regulated AMPs in WSSV infection. (A) Effective knockdown for ALF1-4 and LYZ1-4 in hemocytes by dsRNA was confirmed by qRT-PCR. (B-F) Silencing of AMPs enhanced WSSV infection in shrimp. WSSV was inoculated at 48 h post each AMP silencing. The viral loads in gills were assessed at 24 h (B), 48 h (C), 72 h (D), 96 h (E) and 120 h (F) post-infection via absolute qPCR. (G-H) Survival of WSSV challenged AMP-silenced shrimp and GFP dsRNA treated shrimp. All experiments were performed three times, and similar results were obtained. All the data from B, C, D, E and F were analyzed statistically by student’s T test (NS, not significant; * p

Techniques Used: Infection, Quantitative RT-PCR, Real-time Polymerase Chain Reaction

Increased viral replication levels in the canonical Toll pathway components silenced shrimps. (A) Knockdown efficiencies of the canonical Toll pathway components including MyD88, Tube, Pelle and Dorsal in gills were checked by qRT-PCR. The GFP dsRNA treated shrimp was set as a control. (B) Silencing of the canonical Toll pathway components resulted in enhanced WSSV replication levels in gill tissues. WSSV was inoculated at 48 h post each component silencing, and the viral load was assessed at 48 hpi through absolute qPCR. The experiment was performed three times with similar results. All the data were analyzed statistically by student’s T test (** p
Figure Legend Snippet: Increased viral replication levels in the canonical Toll pathway components silenced shrimps. (A) Knockdown efficiencies of the canonical Toll pathway components including MyD88, Tube, Pelle and Dorsal in gills were checked by qRT-PCR. The GFP dsRNA treated shrimp was set as a control. (B) Silencing of the canonical Toll pathway components resulted in enhanced WSSV replication levels in gill tissues. WSSV was inoculated at 48 h post each component silencing, and the viral load was assessed at 48 hpi through absolute qPCR. The experiment was performed three times with similar results. All the data were analyzed statistically by student’s T test (** p

Techniques Used: Quantitative RT-PCR, Real-time Polymerase Chain Reaction

RNAi screening identifies Toll4 as an antiviral factor against WSSV. (A) Tissue distribution of L . vannamei Tolls (Toll1-9) was analyzed by Semi-RT-PCR, and EF1α was used as a control. (B-C) Knockdown efficiencies of Toll1, Toll2, Toll3, Toll5 and Toll9 in hemocytes (B), and silencing efficiencies of Toll4, Toll6, Toll7 and Toll8 in gills (B) were checked by qRT-PCR. The GFP dsRNA treated shrimp was set as a control. (D) RNAi screening identified shrimp Tolls (LvToll1-9) as potential antiviral (anti-WSSV) factors. WSSV was inoculated at 48 h post each Toll silencing. The viral load was assessed at 48 h post-infection through absolute qPCR. The experiment was repeated three times with similar results. One dot represented 1 shrimp and the horizontal line represented the median of the results. (E) Silencing of Toll4 enhanced shrimps susceptibility to WSSV infection. WSSV was inoculated at 48 h post Toll4 silencing, and the death of shrimp was recorded at every 8 h for cumulative mortality rates analysis. The experiment was repeated three times, and similar results were obtained. The data were analyzed statistically by the Kaplan–Meier plot (log-rank χ 2 test) (** p
Figure Legend Snippet: RNAi screening identifies Toll4 as an antiviral factor against WSSV. (A) Tissue distribution of L . vannamei Tolls (Toll1-9) was analyzed by Semi-RT-PCR, and EF1α was used as a control. (B-C) Knockdown efficiencies of Toll1, Toll2, Toll3, Toll5 and Toll9 in hemocytes (B), and silencing efficiencies of Toll4, Toll6, Toll7 and Toll8 in gills (B) were checked by qRT-PCR. The GFP dsRNA treated shrimp was set as a control. (D) RNAi screening identified shrimp Tolls (LvToll1-9) as potential antiviral (anti-WSSV) factors. WSSV was inoculated at 48 h post each Toll silencing. The viral load was assessed at 48 h post-infection through absolute qPCR. The experiment was repeated three times with similar results. One dot represented 1 shrimp and the horizontal line represented the median of the results. (E) Silencing of Toll4 enhanced shrimps susceptibility to WSSV infection. WSSV was inoculated at 48 h post Toll4 silencing, and the death of shrimp was recorded at every 8 h for cumulative mortality rates analysis. The experiment was repeated three times, and similar results were obtained. The data were analyzed statistically by the Kaplan–Meier plot (log-rank χ 2 test) (** p

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Infection, Real-time Polymerase Chain Reaction

Dorsal nuclear translocation and phosphorylation are induced by WSSV infection. (A) Tissue distribution of Dorsal was analyzed by qRT-PCR. (B) Dorsal nuclear translocation in hemocytes was detected at 1 h, 3 h and 6 h post WSSV infection, and the WSSV untreated hemocytes (0 h) as a control. The hemocytes were collected at 0 h, 1 h, 3 h and 6 h post WSSV infection, deposited onto a glass slide and subjected to immunocytochemical staning by a prepared anti-Dorsal specific antibody, and finally visualized on a confocal laser scanning microscope. (b) Co-localization of Dorsal and Hochest-stained nucleus in hemocytes was calculated by WCIF ImageJ software and analyzed statistically by student’s T test (** p
Figure Legend Snippet: Dorsal nuclear translocation and phosphorylation are induced by WSSV infection. (A) Tissue distribution of Dorsal was analyzed by qRT-PCR. (B) Dorsal nuclear translocation in hemocytes was detected at 1 h, 3 h and 6 h post WSSV infection, and the WSSV untreated hemocytes (0 h) as a control. The hemocytes were collected at 0 h, 1 h, 3 h and 6 h post WSSV infection, deposited onto a glass slide and subjected to immunocytochemical staning by a prepared anti-Dorsal specific antibody, and finally visualized on a confocal laser scanning microscope. (b) Co-localization of Dorsal and Hochest-stained nucleus in hemocytes was calculated by WCIF ImageJ software and analyzed statistically by student’s T test (** p

Techniques Used: Translocation Assay, Infection, Quantitative RT-PCR, Laser-Scanning Microscopy, Staining, Software

AMPs expression levels in Toll4 silenced shrimps upon WSSV infection. (A-B) Expression profiles of Toll4 after WSSV infection in gill (A) and hemocyte (B) were assessed by qRT-PCR. (C-D) AMPs expression patterns responding to the challenge of WSSV, V . parahaemolyticus (as an activator for canonical Toll pathway) and PBS (as a negative control) in gill (C) and hemocyte (D) was detected by qRT-PCR. The horizontal line indicated 2-fold induction threshold. (E-F) Knockdown efficiencies of Toll4 in gill (E) and hemocyte (F) was confirmed by qRT-PCR at 24 and 48 h post dsRNA injection. (G-H) Toll4-knockdown shrimps had impaired AMPs expression levels upon WSSV infection both in gill (G) and hemocyte (H). All experiments were performed three times, and similar results were observed. All the data were analyzed statistically by student’s T test (* p
Figure Legend Snippet: AMPs expression levels in Toll4 silenced shrimps upon WSSV infection. (A-B) Expression profiles of Toll4 after WSSV infection in gill (A) and hemocyte (B) were assessed by qRT-PCR. (C-D) AMPs expression patterns responding to the challenge of WSSV, V . parahaemolyticus (as an activator for canonical Toll pathway) and PBS (as a negative control) in gill (C) and hemocyte (D) was detected by qRT-PCR. The horizontal line indicated 2-fold induction threshold. (E-F) Knockdown efficiencies of Toll4 in gill (E) and hemocyte (F) was confirmed by qRT-PCR at 24 and 48 h post dsRNA injection. (G-H) Toll4-knockdown shrimps had impaired AMPs expression levels upon WSSV infection both in gill (G) and hemocyte (H). All experiments were performed three times, and similar results were observed. All the data were analyzed statistically by student’s T test (* p

Techniques Used: Expressing, Infection, Quantitative RT-PCR, Negative Control, Injection

12) Product Images from "A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis"

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis

Journal: EMBO Reports

doi: 10.1038/embor.2011.81

EHF directly regulates the expression of RUVBL1. ( A ) qRT–PCR analysis of RUVBL1 expression in HCT116 cells transfected with siRNA targeting a scrambled sequence (siCont) or EHF (siEHF1, siEHF2). Before fold-change calculation, values were normalized
Figure Legend Snippet: EHF directly regulates the expression of RUVBL1. ( A ) qRT–PCR analysis of RUVBL1 expression in HCT116 cells transfected with siRNA targeting a scrambled sequence (siCont) or EHF (siEHF1, siEHF2). Before fold-change calculation, values were normalized

Techniques Used: Expressing, Quantitative RT-PCR, Transfection, Sequencing

13) Product Images from "The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders"

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

Journal: eLife

doi: 10.7554/eLife.41770

Characterization of the epistasis relationship between mouse Nr2f1 and lnc-Nr2f1 . ( A ) CRISPR knock out strategy to generate Nr2f1 knockout (Homo) and heterozygous null lines (Het) from the control mES cells (Ctrl). ( B ) qRT-PCR results for lnc-Nr2f1 and Nr2f1 in the Ctrl, Nr2f1 heterozygous null and Nr2f1 knock out day 4 Ngn2 mES-iN. (n = 4 for Ctrl and Homo, n = 6 for Het; n.s. denotes not significant by two tailed t test) ( C ) Western blot showing the level of NR2F1 for individual clones of Ctrl, Het and Homo for day 4 Ngn2 mES-iN. ( D ) Neurite length measurement of the Ngn2 day 3 mES iN cells generated from the Nr2f1 Ctrl, Het or Homo lines. (n = 4 for Ctrl and Homo, n = 6 for Het) (n.s. indicates p
Figure Legend Snippet: Characterization of the epistasis relationship between mouse Nr2f1 and lnc-Nr2f1 . ( A ) CRISPR knock out strategy to generate Nr2f1 knockout (Homo) and heterozygous null lines (Het) from the control mES cells (Ctrl). ( B ) qRT-PCR results for lnc-Nr2f1 and Nr2f1 in the Ctrl, Nr2f1 heterozygous null and Nr2f1 knock out day 4 Ngn2 mES-iN. (n = 4 for Ctrl and Homo, n = 6 for Het; n.s. denotes not significant by two tailed t test) ( C ) Western blot showing the level of NR2F1 for individual clones of Ctrl, Het and Homo for day 4 Ngn2 mES-iN. ( D ) Neurite length measurement of the Ngn2 day 3 mES iN cells generated from the Nr2f1 Ctrl, Het or Homo lines. (n = 4 for Ctrl and Homo, n = 6 for Het) (n.s. indicates p

Techniques Used: CRISPR, Knock-Out, Quantitative RT-PCR, Two Tailed Test, Western Blot, Clone Assay, Generated

QRT-PCR validation of candidate lncRNAs expression. ( A ) Expression detection of candidate lncRNAs by qRT-PCR across early stages of iN cell reprogramming and mouse brain development.
Figure Legend Snippet: QRT-PCR validation of candidate lncRNAs expression. ( A ) Expression detection of candidate lncRNAs by qRT-PCR across early stages of iN cell reprogramming and mouse brain development.

Techniques Used: Quantitative RT-PCR, Expressing

14) Product Images from "Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture"

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Journal: BMC Plant Biology

doi: 10.1186/s12870-018-1545-5

Expression profile of GhGH3s based on RNA-seq and qRT-PCR in various tissue/organs/stages. a Trends in GhGH3 gene expression based on publicly available RNA-seq data. Expression of individual genes are shown for 20 GhGH3s . Numbers on the x-axis indicate days post anthesis, with negative numbers implying days before anthesis. The prefix OV is for ovules and F for fiber. Green, black and red backgrounds represent low, intermediate and high expression levels, respectively. The original RPKM (reads per kilobase per million) values are normalized to 0–1 and shown in boxes. b Pattern of gene expression by qRT-PCR analysis. Expression of allele pairs or individual genes are shown. Values on the y-axis represent relative expression levels while the x-axis indicates days post anthesis. Materials from the field under normal conditions were tagged and sampled. The relative expression levels of GhGH3 genes were measured in roots (R), stems (S), leaves (L), flowers (FL), early stage developing ovules with attached fibers (1, 3, 5 DPA OF, ovules plus fibers), and different stages of detached ovules and fibers (7, 10, 15, 20 DPA O/F, ovules or fibers). GhHis 3 was used as an internal control to normalize the expression data. Error bars show standard deviation calculated from three replicates
Figure Legend Snippet: Expression profile of GhGH3s based on RNA-seq and qRT-PCR in various tissue/organs/stages. a Trends in GhGH3 gene expression based on publicly available RNA-seq data. Expression of individual genes are shown for 20 GhGH3s . Numbers on the x-axis indicate days post anthesis, with negative numbers implying days before anthesis. The prefix OV is for ovules and F for fiber. Green, black and red backgrounds represent low, intermediate and high expression levels, respectively. The original RPKM (reads per kilobase per million) values are normalized to 0–1 and shown in boxes. b Pattern of gene expression by qRT-PCR analysis. Expression of allele pairs or individual genes are shown. Values on the y-axis represent relative expression levels while the x-axis indicates days post anthesis. Materials from the field under normal conditions were tagged and sampled. The relative expression levels of GhGH3 genes were measured in roots (R), stems (S), leaves (L), flowers (FL), early stage developing ovules with attached fibers (1, 3, 5 DPA OF, ovules plus fibers), and different stages of detached ovules and fibers (7, 10, 15, 20 DPA O/F, ovules or fibers). GhHis 3 was used as an internal control to normalize the expression data. Error bars show standard deviation calculated from three replicates

Techniques Used: Expressing, RNA Sequencing Assay, Quantitative RT-PCR, Standard Deviation

Organization of regulatory elements of GhGH3s and their expression in response to phytohormones. a The regulatory region of each GhGH3 gene was analyzed, the numbers indicate the sum of various cis -acting elements response to the same stimuli. b The summary of GhGH3 expression response to treatment with IAA, SA, BL and GA in roots (R) and stems (S). Each orthologous pair from At- and Dt-subgenome of G. hirsutum was designed as a single gene and tested together due to their highly identical sequences. In total, 11 analogue genes standing for 20 GhGH3s were generated and could be divided into 3 subgroups (subgroups 1–3). The expression pattern of 11 analogue genes was detected by qRT-PCR. The relative expression intensity, that is, the ratio of the highest expression level to that of the 0 h control, was allocated into six different grades ranging from suppression shown as black boxes to over 20-fold induction shown as red boxes
Figure Legend Snippet: Organization of regulatory elements of GhGH3s and their expression in response to phytohormones. a The regulatory region of each GhGH3 gene was analyzed, the numbers indicate the sum of various cis -acting elements response to the same stimuli. b The summary of GhGH3 expression response to treatment with IAA, SA, BL and GA in roots (R) and stems (S). Each orthologous pair from At- and Dt-subgenome of G. hirsutum was designed as a single gene and tested together due to their highly identical sequences. In total, 11 analogue genes standing for 20 GhGH3s were generated and could be divided into 3 subgroups (subgroups 1–3). The expression pattern of 11 analogue genes was detected by qRT-PCR. The relative expression intensity, that is, the ratio of the highest expression level to that of the 0 h control, was allocated into six different grades ranging from suppression shown as black boxes to over 20-fold induction shown as red boxes

Techniques Used: Expressing, Generated, Quantitative RT-PCR

15) Product Images from "Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway"

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway

Journal: Animal Cells and Systems

doi: 10.1080/19768354.2017.1289980

The efficiency of siRNA transfection. (A) qRT-PCR (left) and western blotting (right) indicated that knockdown of truncated TrkB with si-r-TrkB-3 could significantly decrease the expression of truncated TrkB in cultured SCs; (B) qRT-PCR (left) and western blotting (right) demonstrated that transfection of siRNAs targeting p75NTR led to efficient knockdown of p75NTR in SCs cells with si-r-p75NTR-2 giving the best knockdown efficiency. * p
Figure Legend Snippet: The efficiency of siRNA transfection. (A) qRT-PCR (left) and western blotting (right) indicated that knockdown of truncated TrkB with si-r-TrkB-3 could significantly decrease the expression of truncated TrkB in cultured SCs; (B) qRT-PCR (left) and western blotting (right) demonstrated that transfection of siRNAs targeting p75NTR led to efficient knockdown of p75NTR in SCs cells with si-r-p75NTR-2 giving the best knockdown efficiency. * p

Techniques Used: Transfection, Quantitative RT-PCR, Western Blot, Expressing, Cell Culture

16) Product Images from "Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags"

Article Title: Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags

Journal: BMC Genomics

doi: 10.1186/1471-2164-10-69

Quantitative Real-time PCR analysis of gene expression in Plectus murrayi in response to desiccation . Values were determined using qRT-PCR and represents relative expression of genes from desiccated to undesiccated nematodes (control). The relative expression of the target gene ( Pm-alh : aldehyde dehydrogenase; Pm-tps : trehalose-6-phosphate synthase; Pm-gpx : glutathione peroxidise; Pm-afp : antifreeze protein; Pm-hsp-70 : heat shock protein 70; Pm-lea : late embryogenesis abundant protein; Pm-gk : glycerol kinase; Pm-ms : malate synthase; Pm-gsy : glycogen synthase; Pm-hsp-90 : heat shock protein 90; Pm-rpl-4 : ribosomal protein-4; Pm-desc-1 : novel protein I; Pm-desc-2 : novel protein II; Pm-gst-1 : glutathione s-transferase 1,) normalized to Pm-18s :18S rRNA and relative to the expression of control, was calculated for each sample using the 2 -ΔΔCT method [ 87 ]. Gene expression was determined in each sample using three independent technical replicates. A transcript with relative abundance of one is equivalent to the abundance of 18S rRNA. Bars represent standard errors calculated from three replicates of each experiment. *Significant difference ( P
Figure Legend Snippet: Quantitative Real-time PCR analysis of gene expression in Plectus murrayi in response to desiccation . Values were determined using qRT-PCR and represents relative expression of genes from desiccated to undesiccated nematodes (control). The relative expression of the target gene ( Pm-alh : aldehyde dehydrogenase; Pm-tps : trehalose-6-phosphate synthase; Pm-gpx : glutathione peroxidise; Pm-afp : antifreeze protein; Pm-hsp-70 : heat shock protein 70; Pm-lea : late embryogenesis abundant protein; Pm-gk : glycerol kinase; Pm-ms : malate synthase; Pm-gsy : glycogen synthase; Pm-hsp-90 : heat shock protein 90; Pm-rpl-4 : ribosomal protein-4; Pm-desc-1 : novel protein I; Pm-desc-2 : novel protein II; Pm-gst-1 : glutathione s-transferase 1,) normalized to Pm-18s :18S rRNA and relative to the expression of control, was calculated for each sample using the 2 -ΔΔCT method [ 87 ]. Gene expression was determined in each sample using three independent technical replicates. A transcript with relative abundance of one is equivalent to the abundance of 18S rRNA. Bars represent standard errors calculated from three replicates of each experiment. *Significant difference ( P

Techniques Used: Real-time Polymerase Chain Reaction, Expressing, Quantitative RT-PCR, Mass Spectrometry

17) Product Images from "CRISPR/Cas9-mediated targeted mutagenesis of GmLHY genes alters plant height and internode length in soybean"

Article Title: CRISPR/Cas9-mediated targeted mutagenesis of GmLHY genes alters plant height and internode length in soybean

Journal: BMC Plant Biology

doi: 10.1186/s12870-019-2145-8

Diurnal expression patterns of GmLHY1a/1b/2a/2b in WT plants and T2 homozygous quadruple mutants of GmLHY . a – d qRT-PCR analysis of GmLHY2b , GmLHY2a, GmLHY1a, and GmLHY1b expression levels in the leaves at 20 DAE under 16 h light/8 h dark (long day; LD) conditions, respectively. Data shown are relative to the control gene GmTUB and represent means ± standard error of the mean (s.e.m.) for three biological replicates. Bars indicate the s.e.m. Black and white bars represent dark and light periods, respectively
Figure Legend Snippet: Diurnal expression patterns of GmLHY1a/1b/2a/2b in WT plants and T2 homozygous quadruple mutants of GmLHY . a – d qRT-PCR analysis of GmLHY2b , GmLHY2a, GmLHY1a, and GmLHY1b expression levels in the leaves at 20 DAE under 16 h light/8 h dark (long day; LD) conditions, respectively. Data shown are relative to the control gene GmTUB and represent means ± standard error of the mean (s.e.m.) for three biological replicates. Bars indicate the s.e.m. Black and white bars represent dark and light periods, respectively

Techniques Used: Expressing, Quantitative RT-PCR

18) Product Images from "Endogenous CHRNA7-ligand SLURP1 as a potential tumor suppressor and anti-nicotinic factor in pancreatic cancer"

Article Title: Endogenous CHRNA7-ligand SLURP1 as a potential tumor suppressor and anti-nicotinic factor in pancreatic cancer

Journal: Oncotarget

doi: 10.18632/oncotarget.24312

High level of circulating SLURP1 is associated with better survival in operable PDAC patients ( A ) The measurement of pancreatic SLURP1 mRNA expression with qRT-PCR in 66 pancreatic samples revealed the lack of expression in non-malignant pancreatic tissues and most PDAC lesions. ( B ) The concentration of SLURP1 was measured in 106 human serum samples using a commercial EIA kit produced by CUSABIO. Multiple comparison testing revealed a lack of difference between the analyzed groups ( p = 0.643). ( C ) Circulating SLURP1 levels correlated with the grade of differentiation but not with any of the TNM parameters. ( D ) Dividing the PDAC patients with resected tumors into SLURP1 high/low groups according to the preoperative level of circulating SLURP1 for the Kaplan-Meier survival analysis revealed significantly longer survival of SLURP1 high patients (cut-off = 16 ng/ml; log-rank test p = 0.007), MS: median survival. ( E ) The concentration of SLURP1 was re-measured in 67 human serum samples using a commercial EIA kit produced by USCN and confirmed the lack of difference between the analyzed groups ( p = 0.951). ( F ) Nevertheless, the USCN-EIA recognized the CUSABIO standard but not vice versa, and the USCN values for SLURP1 were three-fold lower and lacked any correlation with the CUSABIO values. Additional information is presented in Table 1 . ( G ) Clustering analysis of the RNAseq data obtained for the PDAC specimens corresponding to the serum samples with low and high SLURP1 content.
Figure Legend Snippet: High level of circulating SLURP1 is associated with better survival in operable PDAC patients ( A ) The measurement of pancreatic SLURP1 mRNA expression with qRT-PCR in 66 pancreatic samples revealed the lack of expression in non-malignant pancreatic tissues and most PDAC lesions. ( B ) The concentration of SLURP1 was measured in 106 human serum samples using a commercial EIA kit produced by CUSABIO. Multiple comparison testing revealed a lack of difference between the analyzed groups ( p = 0.643). ( C ) Circulating SLURP1 levels correlated with the grade of differentiation but not with any of the TNM parameters. ( D ) Dividing the PDAC patients with resected tumors into SLURP1 high/low groups according to the preoperative level of circulating SLURP1 for the Kaplan-Meier survival analysis revealed significantly longer survival of SLURP1 high patients (cut-off = 16 ng/ml; log-rank test p = 0.007), MS: median survival. ( E ) The concentration of SLURP1 was re-measured in 67 human serum samples using a commercial EIA kit produced by USCN and confirmed the lack of difference between the analyzed groups ( p = 0.951). ( F ) Nevertheless, the USCN-EIA recognized the CUSABIO standard but not vice versa, and the USCN values for SLURP1 were three-fold lower and lacked any correlation with the CUSABIO values. Additional information is presented in Table 1 . ( G ) Clustering analysis of the RNAseq data obtained for the PDAC specimens corresponding to the serum samples with low and high SLURP1 content.

Techniques Used: Expressing, Quantitative RT-PCR, Concentration Assay, Enzyme-linked Immunosorbent Assay, Produced, Mass Spectrometry

Preservation of CHRNA7 expression in the pancreas is associated with better prognosis for operable PDAC patients ( A ) CHRNA7 mRNA expression was determined by qRT-PCR in 66 pancreatic samples obtained from the organ donors and patients with chronic pancreatitis (CP) or pancreatic adenocarcinoma (PDAC). The groups were compared using the Kruskal-Wallis test ( p = 0.004) with Dunn’s procedure, which established significant down-regulation of CHRNA7 in PDAC patients ( p
Figure Legend Snippet: Preservation of CHRNA7 expression in the pancreas is associated with better prognosis for operable PDAC patients ( A ) CHRNA7 mRNA expression was determined by qRT-PCR in 66 pancreatic samples obtained from the organ donors and patients with chronic pancreatitis (CP) or pancreatic adenocarcinoma (PDAC). The groups were compared using the Kruskal-Wallis test ( p = 0.004) with Dunn’s procedure, which established significant down-regulation of CHRNA7 in PDAC patients ( p

Techniques Used: Preserving, Expressing, Quantitative RT-PCR

CHRNA7 is a major binding site for SLURP1 on PDAC cells ( A ) Simultaneous FACS and qRT-PCR analyses revealed CHRNA7-positivity of all eight tested PDAC cell lines, whereby membranous CHRNA7-staining showed significant inter-experimental variability and lack of correlation with RNA levels. The graph summarizes the data of two independent experiments shown below and measuring CHRNA7 mRNA (qRT-PCR; log10-transformed number of transcripts/10k PPIB) and surface protein expression (log10-transformed mean fluorescence intensity/MFI values) in unrelated passages of each cell line. ( B ) Individual FACS histograms illustrating intra- and inter-experimental variability are shown as an overlap of anti-CHRNA7-IgG (gray tinted area) and rabbit IgG (bold black line; isotype control) profiles; the difference in their geometric MFIs was used to calculate final MFI value for each culture. ( C ) qRT-PCR data demonstrating the inter-experimental stability of CHRNA7 mRNA expression also revealed the existence of the two groups, whereby CHRNA7 high -group but not CHRNA7 neg/low -group showed RNA-agreeable, stable pattern of protein expression. ( D – F ) The siRNA-based depletion of CHRNA7 confirmed the specificity of the reagents such as primers (qRT-PCR, D) and antibodies (Western blot, E, and FACS, F). As illustrated for COLO357 cultures, transfection with three commercially available CHRNA7-specific siRNA sets (si#1, si#2, si#3) eliminated over 75% of CHRNA7 mRNA and protein compared to the transfection of cells with negative control siRNA set (neg.si) or left untreated (control). ( G ) siRNA-based depletion of CHRNA7 indicated the preferential binding of SLURP1 to this receptor on PDAC cells. For comparison, FITC-conjugated SLURP1 was added to COLO357 and PANC-1 cells transfected with three different CHRNA7-siRNA sets (‘CHRNA7-depletion’ group depicted by grey-, green- and rose-colored profiles for si#1, si#2 and si#3, respectively) and to cells remaining intact or transfected with negative siRNA (‘controls’ group depicted by blue and lilac-colored profiles).
Figure Legend Snippet: CHRNA7 is a major binding site for SLURP1 on PDAC cells ( A ) Simultaneous FACS and qRT-PCR analyses revealed CHRNA7-positivity of all eight tested PDAC cell lines, whereby membranous CHRNA7-staining showed significant inter-experimental variability and lack of correlation with RNA levels. The graph summarizes the data of two independent experiments shown below and measuring CHRNA7 mRNA (qRT-PCR; log10-transformed number of transcripts/10k PPIB) and surface protein expression (log10-transformed mean fluorescence intensity/MFI values) in unrelated passages of each cell line. ( B ) Individual FACS histograms illustrating intra- and inter-experimental variability are shown as an overlap of anti-CHRNA7-IgG (gray tinted area) and rabbit IgG (bold black line; isotype control) profiles; the difference in their geometric MFIs was used to calculate final MFI value for each culture. ( C ) qRT-PCR data demonstrating the inter-experimental stability of CHRNA7 mRNA expression also revealed the existence of the two groups, whereby CHRNA7 high -group but not CHRNA7 neg/low -group showed RNA-agreeable, stable pattern of protein expression. ( D – F ) The siRNA-based depletion of CHRNA7 confirmed the specificity of the reagents such as primers (qRT-PCR, D) and antibodies (Western blot, E, and FACS, F). As illustrated for COLO357 cultures, transfection with three commercially available CHRNA7-specific siRNA sets (si#1, si#2, si#3) eliminated over 75% of CHRNA7 mRNA and protein compared to the transfection of cells with negative control siRNA set (neg.si) or left untreated (control). ( G ) siRNA-based depletion of CHRNA7 indicated the preferential binding of SLURP1 to this receptor on PDAC cells. For comparison, FITC-conjugated SLURP1 was added to COLO357 and PANC-1 cells transfected with three different CHRNA7-siRNA sets (‘CHRNA7-depletion’ group depicted by grey-, green- and rose-colored profiles for si#1, si#2 and si#3, respectively) and to cells remaining intact or transfected with negative siRNA (‘controls’ group depicted by blue and lilac-colored profiles).

Techniques Used: Binding Assay, FACS, Quantitative RT-PCR, Staining, Transformation Assay, Expressing, Fluorescence, Western Blot, Transfection, Negative Control

19) Product Images from "Crx broadly modulates the pineal transcriptome"

Article Title: Crx broadly modulates the pineal transcriptome

Journal: Journal of neurochemistry

doi: 10.1111/j.1471-4159.2011.07405.x

qRT-PCR analysis of transcripts detected as either day/night expressed or differentially expressed in Crx −/− mice as compared with wild-types
Figure Legend Snippet: qRT-PCR analysis of transcripts detected as either day/night expressed or differentially expressed in Crx −/− mice as compared with wild-types

Techniques Used: Quantitative RT-PCR, Mouse Assay

20) Product Images from "Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice"

Article Title: Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice

Journal: EvoDevo

doi: 10.1186/s13227-017-0065-y

Histological description of early differentiation of African rice panicle and corresponding stages for expression analysis. O. barthii : a – g O. glaberrima : h – n . Developmental stages selected for in situ hybridization and qRT-PCR analyses are indicated in lower panel. Stage 1: unbranched stage with elongation of rachis meristem and formation of primary branch meristems; stage 2: early branching stage with at the end the initiation of spikelet meristem differentiation; stage 3: late branching stage with elongated secondary branch and complete spikelet meristem differentiation; stage 4: floret organ differentiation/development. AM axillary meristem, Fl flower, RM rachis meristem, PBm primary branch meristem, PB primary branch, Sp spikelet. Scale bars 100 µm
Figure Legend Snippet: Histological description of early differentiation of African rice panicle and corresponding stages for expression analysis. O. barthii : a – g O. glaberrima : h – n . Developmental stages selected for in situ hybridization and qRT-PCR analyses are indicated in lower panel. Stage 1: unbranched stage with elongation of rachis meristem and formation of primary branch meristems; stage 2: early branching stage with at the end the initiation of spikelet meristem differentiation; stage 3: late branching stage with elongated secondary branch and complete spikelet meristem differentiation; stage 4: floret organ differentiation/development. AM axillary meristem, Fl flower, RM rachis meristem, PBm primary branch meristem, PB primary branch, Sp spikelet. Scale bars 100 µm

Techniques Used: Expressing, In Situ Hybridization, Quantitative RT-PCR

Expression profiling of branching-related genes at unbranched stage in O. barthii and O. glaberrima . qRT-PCR analysis of OSH1 , LAX1 , SPL14 , APO2, TAW1 , OsMADS22 , OsMADS55 , miR529 and miR156 accumulation levels at stage 1 (unbranched stage with elongation of rachis meristem and formation of primary branch meristems) in O. barthii ( gray lines ) and in O. glaberrima ( orange lines ). Target mRNA and small RNA accumulation levels were normalized using rice Actin gene ( LOC_Os03g50885 ) transcript and mature miR159 microRNA accumulation levels, respectively. For mRNAs, the graph is divided into two sections due to scale range. Statistical significances (i.e., t test) between the two species for the relative expression levels of each gene are as follows: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001
Figure Legend Snippet: Expression profiling of branching-related genes at unbranched stage in O. barthii and O. glaberrima . qRT-PCR analysis of OSH1 , LAX1 , SPL14 , APO2, TAW1 , OsMADS22 , OsMADS55 , miR529 and miR156 accumulation levels at stage 1 (unbranched stage with elongation of rachis meristem and formation of primary branch meristems) in O. barthii ( gray lines ) and in O. glaberrima ( orange lines ). Target mRNA and small RNA accumulation levels were normalized using rice Actin gene ( LOC_Os03g50885 ) transcript and mature miR159 microRNA accumulation levels, respectively. For mRNAs, the graph is divided into two sections due to scale range. Statistical significances (i.e., t test) between the two species for the relative expression levels of each gene are as follows: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001

Techniques Used: Expressing, Quantitative RT-PCR

21) Product Images from "High-density array analysis of DNA methylation in Tamoxifen-resistant breast cancer cell lines"

Article Title: High-density array analysis of DNA methylation in Tamoxifen-resistant breast cancer cell lines

Journal: Epigenetics

doi: 10.4161/epi.27111

Figure 6. Comparison of gene expression and promoter methylation in ZNF350 and MAGED1. Relative mRNA levels measured by qRT-PCR and average percent methylation of the TSS200 regions measured by pyrosequencing of ( A ) ZNF350 and ( B ) MAGED1 in control
Figure Legend Snippet: Figure 6. Comparison of gene expression and promoter methylation in ZNF350 and MAGED1. Relative mRNA levels measured by qRT-PCR and average percent methylation of the TSS200 regions measured by pyrosequencing of ( A ) ZNF350 and ( B ) MAGED1 in control

Techniques Used: Expressing, Methylation, Quantitative RT-PCR

22) Product Images from "Doublecortin-like kinase 1 compromises DNA repair and induces chromosomal instability"

Article Title: Doublecortin-like kinase 1 compromises DNA repair and induces chromosomal instability

Journal: Biochemistry and Biophysics Reports

doi: 10.1016/j.bbrep.2018.10.014

MCF10A cells expressing DCLK1 harbor abnormal chromosomes. A: Whole cell lysates (60 μg of total protein) of parent MCF10A, MCF10A-DCLK1 and MCF10A-DCLK1-K419R cells were immunoblotted by the indicated antibodies. B and C: cDNAs were prepared from parent MCF10A and MCF10A-DCLK1 cells and qRT-PCR was performed for indicated genes. The data were normalized against GAPDH and are shown as mean +/- SD. n.s., not significant; * *, p
Figure Legend Snippet: MCF10A cells expressing DCLK1 harbor abnormal chromosomes. A: Whole cell lysates (60 μg of total protein) of parent MCF10A, MCF10A-DCLK1 and MCF10A-DCLK1-K419R cells were immunoblotted by the indicated antibodies. B and C: cDNAs were prepared from parent MCF10A and MCF10A-DCLK1 cells and qRT-PCR was performed for indicated genes. The data were normalized against GAPDH and are shown as mean +/- SD. n.s., not significant; * *, p

Techniques Used: Expressing, Quantitative RT-PCR

23) Product Images from "NLRP6, decreased in gastric cancer, suppresses tumorigenicity of gastric cancer cells"

Article Title: NLRP6, decreased in gastric cancer, suppresses tumorigenicity of gastric cancer cells

Journal: Cancer Management and Research

doi: 10.2147/CMAR.S182980

Effects of NLRP6 on STAT3 signaling. Notes: ( A ) Immunoblot of phosphorylated STAT3, STAT3, Bcl-2, and MMP-2. Blots are representative of three separate experiments. ( B ) mRNA levels of Bcl-2 and MMP-2 were assessed by qRT-PCR. ( C ) BGC-823 and HGC-27 cells were transfected with a Bcl-2 or an MMP-2 luciferase reporter plasmid. The cells were then cultured for 48 hours before determination of normalized luciferase activity. WT, wild-type cells; vector, cells stably expressed control vector; NLR6, cells stably expressed NLRP6. *** P
Figure Legend Snippet: Effects of NLRP6 on STAT3 signaling. Notes: ( A ) Immunoblot of phosphorylated STAT3, STAT3, Bcl-2, and MMP-2. Blots are representative of three separate experiments. ( B ) mRNA levels of Bcl-2 and MMP-2 were assessed by qRT-PCR. ( C ) BGC-823 and HGC-27 cells were transfected with a Bcl-2 or an MMP-2 luciferase reporter plasmid. The cells were then cultured for 48 hours before determination of normalized luciferase activity. WT, wild-type cells; vector, cells stably expressed control vector; NLR6, cells stably expressed NLRP6. *** P

Techniques Used: Quantitative RT-PCR, Transfection, Luciferase, Plasmid Preparation, Cell Culture, Activity Assay, Stable Transfection

24) Product Images from "Gene Expression Mapping of Histone Deacetylases and Co-factors, and Correlation with Survival Time and 1H-HRMAS Metabolomic Profile in Human Gliomas"

Article Title: Gene Expression Mapping of Histone Deacetylases and Co-factors, and Correlation with Survival Time and 1H-HRMAS Metabolomic Profile in Human Gliomas

Journal: Scientific Reports

doi: 10.1038/srep09087

Quantitative expression of the 18 histone deacetylases (HDACs) and 6 metabolic cofactors in different human brain tumors as indicated. The qRT-PCR data are presented as medians of the gene expression level normalized first to the 18S gene then to non-tumoral specimen (the median of controls was set to 1). The boxplots represent the expression rates ranging from the lowest to the highest value. Outlier values are also represented.
Figure Legend Snippet: Quantitative expression of the 18 histone deacetylases (HDACs) and 6 metabolic cofactors in different human brain tumors as indicated. The qRT-PCR data are presented as medians of the gene expression level normalized first to the 18S gene then to non-tumoral specimen (the median of controls was set to 1). The boxplots represent the expression rates ranging from the lowest to the highest value. Outlier values are also represented.

Techniques Used: Expressing, Quantitative RT-PCR

25) Product Images from "Large G protein α-subunit XLαs limits clathrin-mediated endocytosis and regulates tissue iron levels in vivo"

Article Title: Large G protein α-subunit XLαs limits clathrin-mediated endocytosis and regulates tissue iron levels in vivo

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1712670114

P10 XLKO mice exhibit low serum iron levels with increased iron accumulation in heart. ( A ) Prussian blue staining of iron dextran-injected WT and XLKO mice shows more myocardial iron overload in XLKO samples. ( B ) DAB Perls’ enhanced Prussian blue staining of vehicle-treated samples shows more iron deposition in XLKO samples at baseline. Arrows indicate positive stained cells. Images are representative of six to eight mice per genotype from four independent litters. ( C ) qRT-PCR analysis of TfRc using total RNAs isolated from P10 mouse hearts. ( D ) Serum iron levels in P10 WT and XLKO mice. ( E ) TfRc mRNA levels in P10 WT and XLKO kidneys. ( F ) qRT-PCR analysis of XLαs in P10 kidneys and hearts. qRT-PCR was performed by using β-actin as a reference control. Data represent mean ± SEM, * P
Figure Legend Snippet: P10 XLKO mice exhibit low serum iron levels with increased iron accumulation in heart. ( A ) Prussian blue staining of iron dextran-injected WT and XLKO mice shows more myocardial iron overload in XLKO samples. ( B ) DAB Perls’ enhanced Prussian blue staining of vehicle-treated samples shows more iron deposition in XLKO samples at baseline. Arrows indicate positive stained cells. Images are representative of six to eight mice per genotype from four independent litters. ( C ) qRT-PCR analysis of TfRc using total RNAs isolated from P10 mouse hearts. ( D ) Serum iron levels in P10 WT and XLKO mice. ( E ) TfRc mRNA levels in P10 WT and XLKO kidneys. ( F ) qRT-PCR analysis of XLαs in P10 kidneys and hearts. qRT-PCR was performed by using β-actin as a reference control. Data represent mean ± SEM, * P

Techniques Used: Mouse Assay, Staining, Injection, Quantitative RT-PCR, Isolation

Ablation of XLαs enhances transferrin uptake and iron overload-induced apoptosis. ( A ) Western blot analysis of XLαs and Gsα in clonal control and XLKO Ocy454 cells. ( B ) Densitometry analysis of Gsα immunoreactivity shown in A . ( C ) Ocy454 cells were untreated or treated with transferrin-Alexa Fluor 568 for 30 min, and then analyzed by flow cytometry for transferrin uptake for quantification of the median values of transferrin-Alexa Fluor 568 in treated and untreated cells. ( D ) TfRc mRNA expression levels in control and XLKO Ocy454 cells. qRT-PCR was performed by using β-actin as a reference control ( n = 8 for control cells and n = 16 for XLKO cells from four independent expriments). ( E ) Transferrin uptake in primary cardiomyocytes from P2 WT and XLKO mice. Cells were untreated or treated with transferrin-Alexa Fluor 568 for 30 min and then analyzed by flow cytometry for the median values of transferrin uptake. ( F ) TfRc mRNA expression in primary cardiomyocytes. qRT-PCR was performed by using β-actin as a reference control (WT: n = 13; XLKO: n = 10 for primary cardiomyocytes isolated from three different litters). Data represent mean ± SEM * P
Figure Legend Snippet: Ablation of XLαs enhances transferrin uptake and iron overload-induced apoptosis. ( A ) Western blot analysis of XLαs and Gsα in clonal control and XLKO Ocy454 cells. ( B ) Densitometry analysis of Gsα immunoreactivity shown in A . ( C ) Ocy454 cells were untreated or treated with transferrin-Alexa Fluor 568 for 30 min, and then analyzed by flow cytometry for transferrin uptake for quantification of the median values of transferrin-Alexa Fluor 568 in treated and untreated cells. ( D ) TfRc mRNA expression levels in control and XLKO Ocy454 cells. qRT-PCR was performed by using β-actin as a reference control ( n = 8 for control cells and n = 16 for XLKO cells from four independent expriments). ( E ) Transferrin uptake in primary cardiomyocytes from P2 WT and XLKO mice. Cells were untreated or treated with transferrin-Alexa Fluor 568 for 30 min and then analyzed by flow cytometry for the median values of transferrin uptake. ( F ) TfRc mRNA expression in primary cardiomyocytes. qRT-PCR was performed by using β-actin as a reference control (WT: n = 13; XLKO: n = 10 for primary cardiomyocytes isolated from three different litters). Data represent mean ± SEM * P

Techniques Used: Western Blot, Flow Cytometry, Cytometry, Expressing, Quantitative RT-PCR, Mouse Assay, Isolation

26) Product Images from "Carnosine Prevents Aβ-Induced Oxidative Stress and Inflammation in Microglial Cells: A Key Role of TGF-β1"

Article Title: Carnosine Prevents Aβ-Induced Oxidative Stress and Inflammation in Microglial Cells: A Key Role of TGF-β1

Journal: Cells

doi: 10.3390/cells8010064

Carnosine suppresses the Aβ1-42-induced mRNA expression levels of iNOS, Nox1, and Nox2 and increases the expression of TGF-β1 mRNA. Effects of Aβ1-42 and carnosine (Aβ1-42 + Car (co-treat.) and Aβ1-42 + Car (co-inc.)) on ( A ) iNOS, ( B ) Nox1, ( C ) Nox2, and ( D ) TGF-β1 mRNAs expression were examined by qRT-PCR. The abundance of each mRNA of interest was expressed relative to the abundance of GAPDH-mRNA, as an internal control. As a negative control, a reaction in the absence of cDNA (no template control, NTC) was performed. qRT-PCR amplifications were performed in quadruplicate. Standard deviations are represented by vertical bars. * significantly different from resting cells, p
Figure Legend Snippet: Carnosine suppresses the Aβ1-42-induced mRNA expression levels of iNOS, Nox1, and Nox2 and increases the expression of TGF-β1 mRNA. Effects of Aβ1-42 and carnosine (Aβ1-42 + Car (co-treat.) and Aβ1-42 + Car (co-inc.)) on ( A ) iNOS, ( B ) Nox1, ( C ) Nox2, and ( D ) TGF-β1 mRNAs expression were examined by qRT-PCR. The abundance of each mRNA of interest was expressed relative to the abundance of GAPDH-mRNA, as an internal control. As a negative control, a reaction in the absence of cDNA (no template control, NTC) was performed. qRT-PCR amplifications were performed in quadruplicate. Standard deviations are represented by vertical bars. * significantly different from resting cells, p

Techniques Used: Expressing, Quantitative RT-PCR, Negative Control

27) Product Images from "Selection of Reference Genes for qRT-PCR Analysis of Gene Expression in Stipa grandis during Environmental Stresses"

Article Title: Selection of Reference Genes for qRT-PCR Analysis of Gene Expression in Stipa grandis during Environmental Stresses

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169465

Distribution of Ct values of candidate reference genes in S . grandis plants obtained by qRT-PCR. Ct values for each reference gene are tested in all samples. Boxes represent the first and third quartiles of the data. Red lines across the boxes indicate the median Ct values. Whiskers show the maximum and minimum values.
Figure Legend Snippet: Distribution of Ct values of candidate reference genes in S . grandis plants obtained by qRT-PCR. Ct values for each reference gene are tested in all samples. Boxes represent the first and third quartiles of the data. Red lines across the boxes indicate the median Ct values. Whiskers show the maximum and minimum values.

Techniques Used: Quantitative RT-PCR

Pairwise variation (V) analysis of the reference genes in S . grandis using geNorm. The pairwise variation (Vn/n+1) between the normalization factors NFn and NFn+1 was applied to determine the optimal number of reference genes recommended to normalize qRT-PCR data in S . grandis under various stresses. If the Vn/n+1 values were below 0.15, an additional (n + 1) reference was not required.
Figure Legend Snippet: Pairwise variation (V) analysis of the reference genes in S . grandis using geNorm. The pairwise variation (Vn/n+1) between the normalization factors NFn and NFn+1 was applied to determine the optimal number of reference genes recommended to normalize qRT-PCR data in S . grandis under various stresses. If the Vn/n+1 values were below 0.15, an additional (n + 1) reference was not required.

Techniques Used: Quantitative RT-PCR

28) Product Images from "Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells"

Article Title: Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells

Journal: Oncogene

doi: 10.1038/s41388-018-0144-0

Role of Nestin in highly malignant pancreatic cancer cell lines. a Expression of NES mRNA in the cell lines derived from human pancreatic cancer cell lines was determined by qRT-PCR analysis. b , c Expression of Nestin protein in the cell lines derived from SUIT-2 cells ( b ) and Panc-1 cells ( c ) was determined by immunoblotting. d Expression of Nestin protein in parental SUIT-2 and SUIT-2-3P#2 cells was determined by immunocytochemistry. Enlarged pictures of the middle panels are also shown in the right panels. Scale bars are 100 µm. e Expression of Nestin in SUIT-2-3P#2 cells upon treatment with control or Nestin siRNAs. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, the expression of Nestin protein was determined by immunoblotting. f Cell proliferation assay of the SUIT-2-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. g Expression of Nestin in Panc-1-3P#2 cells. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, expression of Nestin protein was determined by immunoblotting. h Survival of the Panc-1-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. Data are presented as mean (duplicate; a ) and mean ± SD ( f , h ), respectively. * P
Figure Legend Snippet: Role of Nestin in highly malignant pancreatic cancer cell lines. a Expression of NES mRNA in the cell lines derived from human pancreatic cancer cell lines was determined by qRT-PCR analysis. b , c Expression of Nestin protein in the cell lines derived from SUIT-2 cells ( b ) and Panc-1 cells ( c ) was determined by immunoblotting. d Expression of Nestin protein in parental SUIT-2 and SUIT-2-3P#2 cells was determined by immunocytochemistry. Enlarged pictures of the middle panels are also shown in the right panels. Scale bars are 100 µm. e Expression of Nestin in SUIT-2-3P#2 cells upon treatment with control or Nestin siRNAs. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, the expression of Nestin protein was determined by immunoblotting. f Cell proliferation assay of the SUIT-2-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. g Expression of Nestin in Panc-1-3P#2 cells. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, expression of Nestin protein was determined by immunoblotting. h Survival of the Panc-1-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. Data are presented as mean (duplicate; a ) and mean ± SD ( f , h ), respectively. * P

Techniques Used: Expressing, Derivative Assay, Quantitative RT-PCR, Immunocytochemistry, Transfection, Proliferation Assay

Mechanisms of acquisition of the malignant phenotype in vivo. a Morphological features of clones isolated from parental SUIT-2 cells. Scale bars are 50 µm. b , c Expression of E-cadherin in the clones from SUIT-2 cells. Expression of CDH1 mRNA and that of E-cadherin protein were determined by qRT-PCR analysis ( b ) and immunoblotting ( c ), respectively. d Tumor-forming ability of the clones isolated from SUIT-2 cells. An equal number of each clone from parental SUIT-2 cells was inoculated into the pancreas. One month after inoculation, the primary tumor was excised (left) and tumor weight was measured (right). e Morphological features of the 3P cells from each clone. The clone-3P cells were established from each clone with three cycles of orthotopic inoculation. Representative images are shown. Scale bars are 50 µm. f Expression levels of E-cadherin, MMP2, and Nestin in the SUIT-2 clones and 3P clones were determined by qRT-PCR analysis. Data are presented as mean (duplicate; b , f ) and mean ± SD ( d ), respectively. **** P
Figure Legend Snippet: Mechanisms of acquisition of the malignant phenotype in vivo. a Morphological features of clones isolated from parental SUIT-2 cells. Scale bars are 50 µm. b , c Expression of E-cadherin in the clones from SUIT-2 cells. Expression of CDH1 mRNA and that of E-cadherin protein were determined by qRT-PCR analysis ( b ) and immunoblotting ( c ), respectively. d Tumor-forming ability of the clones isolated from SUIT-2 cells. An equal number of each clone from parental SUIT-2 cells was inoculated into the pancreas. One month after inoculation, the primary tumor was excised (left) and tumor weight was measured (right). e Morphological features of the 3P cells from each clone. The clone-3P cells were established from each clone with three cycles of orthotopic inoculation. Representative images are shown. Scale bars are 50 µm. f Expression levels of E-cadherin, MMP2, and Nestin in the SUIT-2 clones and 3P clones were determined by qRT-PCR analysis. Data are presented as mean (duplicate; b , f ) and mean ± SD ( d ), respectively. **** P

Techniques Used: In Vivo, Clone Assay, Isolation, Expressing, Quantitative RT-PCR

Gene expression profiles of pancreatic cancer cell lines. a Gene expression profiles of the cells lines derived from SUIT-2 cells using RNA-seq analysis. The result of the cluster analysis is shown by a dendrogram. b Number of upregulated and downregulated genes (left and right, respectively). The genes were purified as follows: upregulated genes: the fragments per kilobase of exon per million mapped sequence reads (FPKM) in SUIT-2-3P cells or SUIT-2-3sc cells were > 3 and increased more than threefold, compared to the FPKM in parental SUIT-2; downregulated genes: the FPKM in parental SUIT-2 were > 3 and decreased more than twofold, compared to the FPKM in SUIT-2-3P cells or SUIT-2-3sc cells. c Gene ontology analysis of upregulated genes in ( b ). Biological processes activated in both SUIT-2-3P and SUIT-2-3sc cells (top) and specifically in SUIT-2-3P cells (bottom) are shown. P -values for comparison between parental SUIT-2 and SUIT-2-3P cells are shown. d Gene expression profiles of the cell lines derived from Panc-1 cells obtained by RNA-seq analyses. The result of the cluster analysis is shown by a dendrogram. e Gene ontology analysis of upregulated genes in Panc-1 cells. Biological processes activated in Panc-1-3P cells are shown. P -values for comparison between parental Panc-1 and Panc-1-3P cells are shown. f Three patterns for upregulation of gene expression in each cancer cell line. Expression levels of MMP2 , ABCG2 , and KRT5 mRNA were determined by qRT-PCR analysis. Data are presented as mean (duplicate; f )
Figure Legend Snippet: Gene expression profiles of pancreatic cancer cell lines. a Gene expression profiles of the cells lines derived from SUIT-2 cells using RNA-seq analysis. The result of the cluster analysis is shown by a dendrogram. b Number of upregulated and downregulated genes (left and right, respectively). The genes were purified as follows: upregulated genes: the fragments per kilobase of exon per million mapped sequence reads (FPKM) in SUIT-2-3P cells or SUIT-2-3sc cells were > 3 and increased more than threefold, compared to the FPKM in parental SUIT-2; downregulated genes: the FPKM in parental SUIT-2 were > 3 and decreased more than twofold, compared to the FPKM in SUIT-2-3P cells or SUIT-2-3sc cells. c Gene ontology analysis of upregulated genes in ( b ). Biological processes activated in both SUIT-2-3P and SUIT-2-3sc cells (top) and specifically in SUIT-2-3P cells (bottom) are shown. P -values for comparison between parental SUIT-2 and SUIT-2-3P cells are shown. d Gene expression profiles of the cell lines derived from Panc-1 cells obtained by RNA-seq analyses. The result of the cluster analysis is shown by a dendrogram. e Gene ontology analysis of upregulated genes in Panc-1 cells. Biological processes activated in Panc-1-3P cells are shown. P -values for comparison between parental Panc-1 and Panc-1-3P cells are shown. f Three patterns for upregulation of gene expression in each cancer cell line. Expression levels of MMP2 , ABCG2 , and KRT5 mRNA were determined by qRT-PCR analysis. Data are presented as mean (duplicate; f )

Techniques Used: Expressing, Derivative Assay, RNA Sequencing Assay, Purification, Sequencing, Quantitative RT-PCR

Characterization of highly malignant cancer cell lines derived from SUIT-2 cells. a Cell proliferation assay of the cell lines derived from SUIT-2 cells. Cells were seeded into 96-well plates and cultured for 2–4 d. Relative absorbance (450–595 nm) at the indicated days is shown. b Morphological features of the cell lines derived from SUIT-2 cells. Scale bars are 50 µm. c , d Expression of E-cadherin in the cell lines derived from SUIT-2 cells. Expression levels of CDH1 mRNA and amounts of E-cadherin protein were determined by qRT-PCR analysis ( c ) and immunoblotting ( d ), respectively. e Adhesion assay of the cell lines derived from SUIT-2 cells. Cells were seeded into fibronectin-coated 96-well plates under the FBS-free conditions and cultured for 30 min. The images of adhered cells (left) and the absorbance at 570 nm (right) are shown. f Chamber migration assay of the cell lines derived from SUIT-2 cells. Cells were seeded into the chamber and incubated for 24 h. The representative images (left) and the number of migrated cells (right) are shown. Scale bars are 100 µm. Data are presented as mean (duplicate; c ) and mean ± SD ( e , f ), respectively. ** P
Figure Legend Snippet: Characterization of highly malignant cancer cell lines derived from SUIT-2 cells. a Cell proliferation assay of the cell lines derived from SUIT-2 cells. Cells were seeded into 96-well plates and cultured for 2–4 d. Relative absorbance (450–595 nm) at the indicated days is shown. b Morphological features of the cell lines derived from SUIT-2 cells. Scale bars are 50 µm. c , d Expression of E-cadherin in the cell lines derived from SUIT-2 cells. Expression levels of CDH1 mRNA and amounts of E-cadherin protein were determined by qRT-PCR analysis ( c ) and immunoblotting ( d ), respectively. e Adhesion assay of the cell lines derived from SUIT-2 cells. Cells were seeded into fibronectin-coated 96-well plates under the FBS-free conditions and cultured for 30 min. The images of adhered cells (left) and the absorbance at 570 nm (right) are shown. f Chamber migration assay of the cell lines derived from SUIT-2 cells. Cells were seeded into the chamber and incubated for 24 h. The representative images (left) and the number of migrated cells (right) are shown. Scale bars are 100 µm. Data are presented as mean (duplicate; c ) and mean ± SD ( e , f ), respectively. ** P

Techniques Used: Derivative Assay, Proliferation Assay, Cell Culture, Expressing, Quantitative RT-PCR, Cell Adhesion Assay, Migration, Incubation

29) Product Images from "Effect of Sodium Butyrate on LHX1 mRNA Expression as a Transcription Factor of HDAC8 in Human Colorectal Cancer Cell Lines"

Article Title: Effect of Sodium Butyrate on LHX1 mRNA Expression as a Transcription Factor of HDAC8 in Human Colorectal Cancer Cell Lines

Journal: Avicenna Journal of Medical Biotechnology

doi:

The Effect of sodium butyrate (SB) on LHX1 mRNA expression in HCT-116 cell line. A) Cells were cultured for 24 hr with 6.25 mM to 100 mM of SB at 37 °C . B) Cells were cultured for 48 hr with 6.25 mM 100 mM of SB at 37 °C . LHX1 mRNA expression investigated using qRT-PCR. GAPDH was used as an internal control. LHX1 mRNA expression decreased in treated cells compared to control (0 mM ). * Indicates a significant reduction (p
Figure Legend Snippet: The Effect of sodium butyrate (SB) on LHX1 mRNA expression in HCT-116 cell line. A) Cells were cultured for 24 hr with 6.25 mM to 100 mM of SB at 37 °C . B) Cells were cultured for 48 hr with 6.25 mM 100 mM of SB at 37 °C . LHX1 mRNA expression investigated using qRT-PCR. GAPDH was used as an internal control. LHX1 mRNA expression decreased in treated cells compared to control (0 mM ). * Indicates a significant reduction (p

Techniques Used: Expressing, Cell Culture, Quantitative RT-PCR

The effect of sodium butyrate (SB) on the LHX1 mRNA expression in HT-29 cell line. A) Cells were cultured for 24 hr with 6.25 to 100 mM concentrations of SB at 37 °C . B) Cells were cultured for 48 hr with 6.25 to 100 mM concentrations of SB at 37 °C . LHX1 mRNA expression was investigated using qRT-PCR. GAPDH was used as the internal control. LHX1 mRNA expression increased in treated cells compared to control (0 mM ). * Indicates a significant increase (p
Figure Legend Snippet: The effect of sodium butyrate (SB) on the LHX1 mRNA expression in HT-29 cell line. A) Cells were cultured for 24 hr with 6.25 to 100 mM concentrations of SB at 37 °C . B) Cells were cultured for 48 hr with 6.25 to 100 mM concentrations of SB at 37 °C . LHX1 mRNA expression was investigated using qRT-PCR. GAPDH was used as the internal control. LHX1 mRNA expression increased in treated cells compared to control (0 mM ). * Indicates a significant increase (p

Techniques Used: Expressing, Cell Culture, Quantitative RT-PCR

30) Product Images from "Drought Tolerance Is Correlated with the Activity of Antioxidant Enzymes in Cerasus humilis Seedlings"

Article Title: Drought Tolerance Is Correlated with the Activity of Antioxidant Enzymes in Cerasus humilis Seedlings

Journal: BioMed Research International

doi: 10.1155/2016/9851095

Effects of water stress (WS) on expression pattern of cytosol APX (cAPX) (a) and dehydroascorbate reductase (DHAR) (b) in Cerasus humilis leaves of Huai'rou (HR) and Nongda4 (ND4) by qRT-PCR. Data are the means of at least five replicates with standard errors shown by vertical bars. Asterisk ( ∗ ) indicates significant difference with control groups (well-watered) at the 0.05 level of probability by Duncan's Multiple-Range Test.
Figure Legend Snippet: Effects of water stress (WS) on expression pattern of cytosol APX (cAPX) (a) and dehydroascorbate reductase (DHAR) (b) in Cerasus humilis leaves of Huai'rou (HR) and Nongda4 (ND4) by qRT-PCR. Data are the means of at least five replicates with standard errors shown by vertical bars. Asterisk ( ∗ ) indicates significant difference with control groups (well-watered) at the 0.05 level of probability by Duncan's Multiple-Range Test.

Techniques Used: Expressing, Quantitative RT-PCR

31) Product Images from "Helicobacter pylori Vacuolating Cytotoxin A Causes Anorexia and Anxiety via Hypothalamic Urocortin 1 in Mice"

Article Title: Helicobacter pylori Vacuolating Cytotoxin A Causes Anorexia and Anxiety via Hypothalamic Urocortin 1 in Mice

Journal: Scientific Reports

doi: 10.1038/s41598-019-42163-4

Peripheral VacA administration induces anorexia, anxiety, and the mRNA expression of Ucn1 in mice. ( a) Cumulative food intake was measured for 24 h in mice receiving IP administration ( n = 8–10). ( b , c ) The percentage of time spent in the open arms ( b ) and total distance ( c ) were measured 4 h after the IP administration of 30 nmol/kg bw of VacA in mice ( n = 5–8). TBS (vehicle) was administered as the control. ( d ) Four hours after IP administration of 30 nmol/kg bw of VacA to mice, the orexigenic and anorexigenic peptide mRNA levels in the hypothalamus were measured by qRT-PCR ( n = 5–8). The values are presented as the means ± SEM. Differences were considered significant at * p
Figure Legend Snippet: Peripheral VacA administration induces anorexia, anxiety, and the mRNA expression of Ucn1 in mice. ( a) Cumulative food intake was measured for 24 h in mice receiving IP administration ( n = 8–10). ( b , c ) The percentage of time spent in the open arms ( b ) and total distance ( c ) were measured 4 h after the IP administration of 30 nmol/kg bw of VacA in mice ( n = 5–8). TBS (vehicle) was administered as the control. ( d ) Four hours after IP administration of 30 nmol/kg bw of VacA to mice, the orexigenic and anorexigenic peptide mRNA levels in the hypothalamus were measured by qRT-PCR ( n = 5–8). The values are presented as the means ± SEM. Differences were considered significant at * p

Techniques Used: Expressing, Mouse Assay, Quantitative RT-PCR

32) Product Images from "Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways"

Article Title: Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways

Journal: Human Molecular Genetics

doi: 10.1093/hmg/ddv315

Quantification of DUX4 activation events and DUX4 and DUX4 target mRNA expression analysis in sorted myoblasts. ( A ) Representative flow cytometry plots of BFP fluorescence intensity (X-axis) versus autofluorescence (Y-axis) in 72 h differentiated control and FSHD myoblasts harboring the DUX4-activated BFP reporter with % reporter + cells displayed for each line. ( B ) Populations of BFP+ and BFP– myoblasts were collected by flow sorting and mRNA levels of DUX4, and DUX4 targets BFP, CCNA1 and MBD3L2 were measured by qRT-PCR. (N.D., not detected).
Figure Legend Snippet: Quantification of DUX4 activation events and DUX4 and DUX4 target mRNA expression analysis in sorted myoblasts. ( A ) Representative flow cytometry plots of BFP fluorescence intensity (X-axis) versus autofluorescence (Y-axis) in 72 h differentiated control and FSHD myoblasts harboring the DUX4-activated BFP reporter with % reporter + cells displayed for each line. ( B ) Populations of BFP+ and BFP– myoblasts were collected by flow sorting and mRNA levels of DUX4, and DUX4 targets BFP, CCNA1 and MBD3L2 were measured by qRT-PCR. (N.D., not detected).

Techniques Used: Activation Assay, Expressing, Flow Cytometry, Cytometry, Fluorescence, Quantitative RT-PCR

Characterization of a DUX4-activated fluorescent reporter. ( A ) A schematic diagram of the lentiviral vector encoding a DUX4 reporter with five unique DUX4 binding site sequences, identified from individual DUX4 genomic targets and a TATA box located upstream of the sequence for nuclear-localized Blue Fluorescent Protein (nuBFP). A pTK and neomycin phosphotransferase gene (NEO) were included to allow for selection of transduced cells. ( B ) BFP is specifically present in MHC-positive myotubes (green) derived from individuals with FSHD and co-localizes with DUX4 protein (red) by immunofluorescence. ( C ) Delivery of an siRNA targeting the DUX4 transcript (siDUX4) during FSHD myoblast differentiation prohibits BFP reporter activation by eliminating DUX4 protein expression. A universal non-targeting control siRNA (siCTRL) transfected in parallel results in BFP and DUX4 expression typical of FSHD myotubes. ( D ) qRT-PCR of DUX4 and DUX4 targets BFP, CCNA1 and MBD3L2 shows reduced mRNA levels after siDUX4 delivery during FSHD myoblast differentiation. DUX4 and DUX4 target mRNA levels are typical of FSHD cells when siDUX4 is substituted with siCTRL. (N.D., not detected). (E) Immunostaining of endogenous DUX4 target ZNF217 (red) co-localizes with BFP fluorescence (blue) during FSHD myoblast differentiation.
Figure Legend Snippet: Characterization of a DUX4-activated fluorescent reporter. ( A ) A schematic diagram of the lentiviral vector encoding a DUX4 reporter with five unique DUX4 binding site sequences, identified from individual DUX4 genomic targets and a TATA box located upstream of the sequence for nuclear-localized Blue Fluorescent Protein (nuBFP). A pTK and neomycin phosphotransferase gene (NEO) were included to allow for selection of transduced cells. ( B ) BFP is specifically present in MHC-positive myotubes (green) derived from individuals with FSHD and co-localizes with DUX4 protein (red) by immunofluorescence. ( C ) Delivery of an siRNA targeting the DUX4 transcript (siDUX4) during FSHD myoblast differentiation prohibits BFP reporter activation by eliminating DUX4 protein expression. A universal non-targeting control siRNA (siCTRL) transfected in parallel results in BFP and DUX4 expression typical of FSHD myotubes. ( D ) qRT-PCR of DUX4 and DUX4 targets BFP, CCNA1 and MBD3L2 shows reduced mRNA levels after siDUX4 delivery during FSHD myoblast differentiation. DUX4 and DUX4 target mRNA levels are typical of FSHD cells when siDUX4 is substituted with siCTRL. (N.D., not detected). (E) Immunostaining of endogenous DUX4 target ZNF217 (red) co-localizes with BFP fluorescence (blue) during FSHD myoblast differentiation.

Techniques Used: Plasmid Preparation, Binding Assay, Sequencing, Selection, Derivative Assay, Immunofluorescence, Activation Assay, Expressing, Transfection, Quantitative RT-PCR, Immunostaining, Fluorescence

33) Product Images from "Comparative transcriptome analysis reveals host-associated differentiation in Chilo suppressalis (Lepidoptera: Crambidae)"

Article Title: Comparative transcriptome analysis reveals host-associated differentiation in Chilo suppressalis (Lepidoptera: Crambidae)

Journal: Scientific Reports

doi: 10.1038/s41598-017-14137-x

Comparison of gene expression patterns obtained by RNA-Seq and qRT-PCR. Log-fold changes are expressed as the ratio of gene expression after normalization to actinA1 .
Figure Legend Snippet: Comparison of gene expression patterns obtained by RNA-Seq and qRT-PCR. Log-fold changes are expressed as the ratio of gene expression after normalization to actinA1 .

Techniques Used: Expressing, RNA Sequencing Assay, Quantitative RT-PCR

34) Product Images from "Role of Glutaredoxin1 and Glutathione in Regulating the Activity of the Copper-transporting P-type ATPases, ATP7A and ATP7B *"

Article Title: Role of Glutaredoxin1 and Glutathione in Regulating the Activity of the Copper-transporting P-type ATPases, ATP7A and ATP7B *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.154468

Cu accumulation in HEK293T cells following siRNA-mediated knockdown of GRX1 . A , quantitation of GRX1 knockdown assessed by QRT-PCR. HEK293T cells were transiently transfected with the control siRNA plasmid (pSilencer 4.1-CMV puro) or plasmid-encoded GRX1 -targeted hairpin siRNAs (GRX1–9/10, GRX1–11/12, and GRX1–9/10 + 11/12). GRX1 mRNA levels in each culture were compared using normalization to 18 S rRNA levels by the ΔΔCt method. Data are expressed as the mean ± S.E. ( error bars ; n = 6) and were consistent over two independent experiments. Asterisks indicate values that are significantly different: *, p
Figure Legend Snippet: Cu accumulation in HEK293T cells following siRNA-mediated knockdown of GRX1 . A , quantitation of GRX1 knockdown assessed by QRT-PCR. HEK293T cells were transiently transfected with the control siRNA plasmid (pSilencer 4.1-CMV puro) or plasmid-encoded GRX1 -targeted hairpin siRNAs (GRX1–9/10, GRX1–11/12, and GRX1–9/10 + 11/12). GRX1 mRNA levels in each culture were compared using normalization to 18 S rRNA levels by the ΔΔCt method. Data are expressed as the mean ± S.E. ( error bars ; n = 6) and were consistent over two independent experiments. Asterisks indicate values that are significantly different: *, p

Techniques Used: Quantitation Assay, Quantitative RT-PCR, Transfection, Plasmid Preparation

35) Product Images from "Uncovering co-expression gene network modules regulating fruit acidity in diverse apples"

Article Title: Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

Journal: BMC Genomics

doi: 10.1186/s12864-015-1816-6

Expression confirmation of eight selected genes using qRT-PCR. a - h The normalized expression of target genes relative to a control gene (actin) in qRT-PCR was shown in light grey , and their corresponding RPKM values from RNA-seq were in black . The correlation coefficient ( r ) and associated p value ( n = 10) were shown accordingly. Standard deviations were shown with the error bars
Figure Legend Snippet: Expression confirmation of eight selected genes using qRT-PCR. a - h The normalized expression of target genes relative to a control gene (actin) in qRT-PCR was shown in light grey , and their corresponding RPKM values from RNA-seq were in black . The correlation coefficient ( r ) and associated p value ( n = 10) were shown accordingly. Standard deviations were shown with the error bars

Techniques Used: Expressing, Quantitative RT-PCR, RNA Sequencing Assay

36) Product Images from "Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora"

Article Title: Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora

Journal: BMC Genomics

doi: 10.1186/1471-2164-10-609

Comparison of expression of representative genes selected from microarray data with qRT-PCR . Comparison of fold change values from microarray data with expression ratios calculated from qRT-PCR. Values were determined using qRT-PCR and represents relative expression of genes between L5M and OHB. The relative expression of the target gene ( Hb-sec-23 : Yeast sec homolog, Hb-co-II : Cytochrome c oxidase II, Hb-dao-3 : Dauer or aging adult overexpression, Hb-unc-68 : Uncoordinated, Hb-asp-3 : Aspartyl protease, Hb-hid-1 : High temperature induced dauer formation, Hb-fat-2 : Fatty acid desaturase, Hb-daf-21 : Abnormal dauer formation, Hb-rab-33 : RAB family member, Hb-spl-1 : Sphingosine-1-phosphate lyase) normalized to Hb-18s :18S rRNA and relative to the expression of control. Bars represent standard errors calculated from 4 replicates of each experiment. *Significant difference ( P
Figure Legend Snippet: Comparison of expression of representative genes selected from microarray data with qRT-PCR . Comparison of fold change values from microarray data with expression ratios calculated from qRT-PCR. Values were determined using qRT-PCR and represents relative expression of genes between L5M and OHB. The relative expression of the target gene ( Hb-sec-23 : Yeast sec homolog, Hb-co-II : Cytochrome c oxidase II, Hb-dao-3 : Dauer or aging adult overexpression, Hb-unc-68 : Uncoordinated, Hb-asp-3 : Aspartyl protease, Hb-hid-1 : High temperature induced dauer formation, Hb-fat-2 : Fatty acid desaturase, Hb-daf-21 : Abnormal dauer formation, Hb-rab-33 : RAB family member, Hb-spl-1 : Sphingosine-1-phosphate lyase) normalized to Hb-18s :18S rRNA and relative to the expression of control. Bars represent standard errors calculated from 4 replicates of each experiment. *Significant difference ( P

Techniques Used: Expressing, Microarray, Quantitative RT-PCR, Size-exclusion Chromatography, Over Expression

Correlation between the fold change values from microarray and the expression ratios calculated from qRT-PCR presented as level of gene expression . Correlation coefficient between the fold change values from microarray and qRT-PCR.
Figure Legend Snippet: Correlation between the fold change values from microarray and the expression ratios calculated from qRT-PCR presented as level of gene expression . Correlation coefficient between the fold change values from microarray and qRT-PCR.

Techniques Used: Microarray, Expressing, Quantitative RT-PCR

37) Product Images from "A20 plays a critical role in the immunoregulatory function of mesenchymal stem cells"

Article Title: A20 plays a critical role in the immunoregulatory function of mesenchymal stem cells

Journal: Journal of Cellular and Molecular Medicine

doi: 10.1111/jcmm.12849

Proliferation and differentiation capacities of sh CTRL C3 MSC s and shA20 C3 MSC s. ( A ) BrdU incorporation coupled with 7 AAD staining was analysed by flow cytometry. C3 MSC s were cultured in ( B ) osteogenic or ( C ) adipogenic differentiation medium for 14 days, and stained with ALP (bar = 100 μm) or Oil Red O (bar = 50 μm). ( D ) C3 MSC s cultured in osteogenic or adipogenic medium for the indicated times were analysed for ALP , Osterix, PPAR ‐γ and aP 2 by qRT ‐ PCR , ** P
Figure Legend Snippet: Proliferation and differentiation capacities of sh CTRL C3 MSC s and shA20 C3 MSC s. ( A ) BrdU incorporation coupled with 7 AAD staining was analysed by flow cytometry. C3 MSC s were cultured in ( B ) osteogenic or ( C ) adipogenic differentiation medium for 14 days, and stained with ALP (bar = 100 μm) or Oil Red O (bar = 50 μm). ( D ) C3 MSC s cultured in osteogenic or adipogenic medium for the indicated times were analysed for ALP , Osterix, PPAR ‐γ and aP 2 by qRT ‐ PCR , ** P

Techniques Used: BrdU Incorporation Assay, Staining, Flow Cytometry, Cytometry, Cell Culture, ALP Assay, Quantitative RT-PCR

Morphological and phenotypic characterization of C3 MSC s after A20 knockdown. ( A ) qRT ‐ PCR analysis of A20 mRNA levels with or without A20 knockdown. ( B ) Morphology and ( C ) size of cultured sh CTRL C3 MSC s and shA20 C3 MSC s were analysed by microscopy and flow cytometry. ( D ) Cell surface markers were analysed by flow cytometry, ** P
Figure Legend Snippet: Morphological and phenotypic characterization of C3 MSC s after A20 knockdown. ( A ) qRT ‐ PCR analysis of A20 mRNA levels with or without A20 knockdown. ( B ) Morphology and ( C ) size of cultured sh CTRL C3 MSC s and shA20 C3 MSC s were analysed by microscopy and flow cytometry. ( D ) Cell surface markers were analysed by flow cytometry, ** P

Techniques Used: Quantitative RT-PCR, Cell Culture, Microscopy, Flow Cytometry, Cytometry

Inflammatory cytokines induce A20 expression in MSC s. MSC s ( A ) and C3H/10T1/2 ( B and C ) were treated with 0, 2, 5 and 10 ng/ml IFN ‐γ and TNF ‐α for 24 hrs. A20 mRNA and protein levels were examined by qRT ‐ PCR and Western blot analysis. MSC s ( D ) and C3H/10T1/2 ( E and F ) were treated with 5 ng/ml IFN ‐γ and TNF ‐α for 0, 6, 12 and 24 hrs, and mRNA and protein expression levels were determined by qRT ‐ PCR and Western blot analysis, respectively.
Figure Legend Snippet: Inflammatory cytokines induce A20 expression in MSC s. MSC s ( A ) and C3H/10T1/2 ( B and C ) were treated with 0, 2, 5 and 10 ng/ml IFN ‐γ and TNF ‐α for 24 hrs. A20 mRNA and protein levels were examined by qRT ‐ PCR and Western blot analysis. MSC s ( D ) and C3H/10T1/2 ( E and F ) were treated with 5 ng/ml IFN ‐γ and TNF ‐α for 0, 6, 12 and 24 hrs, and mRNA and protein expression levels were determined by qRT ‐ PCR and Western blot analysis, respectively.

Techniques Used: Expressing, Quantitative RT-PCR, Western Blot

A20 inhibits TNF ‐α and promotes IL ‐10 production in C3 MSC s, and the p38/ MAPK pathway is involved in A20‐induced immunomodulation. TNF ‐α ( A ) and IL ‐10 ( B , left) expression was examined with or without stimulation with 5 ng/ml IFN ‐γ and TNF ‐α by qRT ‐ PCR . IL ‐10 protein level was determined by ELISA ( B , right). ( C ) The time courses of p38 phosphorylation in response to 5 ng/ml IFN ‐γ and TNF ‐α was determined by immunoblotting, ** P
Figure Legend Snippet: A20 inhibits TNF ‐α and promotes IL ‐10 production in C3 MSC s, and the p38/ MAPK pathway is involved in A20‐induced immunomodulation. TNF ‐α ( A ) and IL ‐10 ( B , left) expression was examined with or without stimulation with 5 ng/ml IFN ‐γ and TNF ‐α by qRT ‐ PCR . IL ‐10 protein level was determined by ELISA ( B , right). ( C ) The time courses of p38 phosphorylation in response to 5 ng/ml IFN ‐γ and TNF ‐α was determined by immunoblotting, ** P

Techniques Used: Expressing, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

38) Product Images from "Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development"

Article Title: Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development

Journal: PeerJ

doi: 10.7717/peerj.8259

Correlation analysis of qRT-PCR and RNA-Seq data.
Figure Legend Snippet: Correlation analysis of qRT-PCR and RNA-Seq data.

Techniques Used: Quantitative RT-PCR, RNA Sequencing Assay

39) Product Images from "Oocyte-specific deletion of furin leads to female infertility by causing early secondary follicle arrest in mice"

Article Title: Oocyte-specific deletion of furin leads to female infertility by causing early secondary follicle arrest in mice

Journal: Cell Death & Disease

doi: 10.1038/cddis.2017.231

Oocyte-specific deletion of furin causes loss of the mature form of ADAMTS1 in oocytes. ( a ) qRT-PCR analysis of the mRNA expression of ADAMTS-1 in oocytes with the indicated genotypes. ** P
Figure Legend Snippet: Oocyte-specific deletion of furin causes loss of the mature form of ADAMTS1 in oocytes. ( a ) qRT-PCR analysis of the mRNA expression of ADAMTS-1 in oocytes with the indicated genotypes. ** P

Techniques Used: Quantitative RT-PCR, Expressing

Localization and oocyte-specific deletion of furin . ( a ) Representative images of subcellular localization of FURIN in GV oocytes. Oocytes were immunolabeled with FURIN antibody (green) and counterstained with propidium iodide (PI) (red) for DNA. GV, germinal vesicle. Scale bar=20 μ m. ( b ) FURIN IHC staining showing the localization during follicular development in the mouse ovary. Scale bar=100 μ m. ( c ) qRT-PCR showing furin mRNA level in fur fl/fl and fur fl/fl ; Zp3-Cre oocytes, respectively ( n =3 for each genotype). ** P
Figure Legend Snippet: Localization and oocyte-specific deletion of furin . ( a ) Representative images of subcellular localization of FURIN in GV oocytes. Oocytes were immunolabeled with FURIN antibody (green) and counterstained with propidium iodide (PI) (red) for DNA. GV, germinal vesicle. Scale bar=20 μ m. ( b ) FURIN IHC staining showing the localization during follicular development in the mouse ovary. Scale bar=100 μ m. ( c ) qRT-PCR showing furin mRNA level in fur fl/fl and fur fl/fl ; Zp3-Cre oocytes, respectively ( n =3 for each genotype). ** P

Techniques Used: Immunolabeling, Immunohistochemistry, Staining, Quantitative RT-PCR

40) Product Images from "Generation of Pigs Resistant to Highly Pathogenic-Porcine Reproductive and Respiratory Syndrome Virus through Gene Editing of CD163"

Article Title: Generation of Pigs Resistant to Highly Pathogenic-Porcine Reproductive and Respiratory Syndrome Virus through Gene Editing of CD163

Journal: International Journal of Biological Sciences

doi: 10.7150/ijbs.25862

CD163 Mut/Mut PAMs are remarkably resistant to HP-PRRSV infection . (A) After infection with the HP-PRRSV strain JXwn06 at the indicated MOIs (0.005, 0.025, 0.1, 0.25, 2.0), culture supernatants were collected at 36 hpi, and viral titers were analyzed by a standard TCID 50 assay (left). Cells were collected to measure relative expression of viral RNA by qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (B) After infection with HP-PRRSV strain JXwn06 at an MOI of 0.1, viral titers were measured by TCID 50 at the indicated time points (12, 24, 36 and 48 h) (left). Relative expression of viral RNA was analyzed using qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (C) PAMs were infected with JXwn06 at an MOI of 0.1, and 36 h later, levels of PRRSV protein GP5 were analyzed by Western blotting analysis (left). Expression of α-tubulin was shown as a loading control. After 48 h, cells were fixed for detection of PRRSV N protein (Green) by immunofluorescent staining(right). The nuclei (blue) were stained with DAPI. (D) The in vitro infection experiment was carried out with the HP-PRRSV strain WUH3. At the indicated MOIs (0.005, 0.025, 0.1, 0.25, 1.0), viral titers were analyzed by a standard TCID 50 assay (left). After infection at an MOI of 0.025, relative expression of viral RNA was analyzed using qRT-PCR at the indicated time points (12, 24, 36, 48, 60 and 72 h). GAPDH mRNA was used as an endogenous control. Data are presented as the mean±SD, n=3. * P
Figure Legend Snippet: CD163 Mut/Mut PAMs are remarkably resistant to HP-PRRSV infection . (A) After infection with the HP-PRRSV strain JXwn06 at the indicated MOIs (0.005, 0.025, 0.1, 0.25, 2.0), culture supernatants were collected at 36 hpi, and viral titers were analyzed by a standard TCID 50 assay (left). Cells were collected to measure relative expression of viral RNA by qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (B) After infection with HP-PRRSV strain JXwn06 at an MOI of 0.1, viral titers were measured by TCID 50 at the indicated time points (12, 24, 36 and 48 h) (left). Relative expression of viral RNA was analyzed using qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (C) PAMs were infected with JXwn06 at an MOI of 0.1, and 36 h later, levels of PRRSV protein GP5 were analyzed by Western blotting analysis (left). Expression of α-tubulin was shown as a loading control. After 48 h, cells were fixed for detection of PRRSV N protein (Green) by immunofluorescent staining(right). The nuclei (blue) were stained with DAPI. (D) The in vitro infection experiment was carried out with the HP-PRRSV strain WUH3. At the indicated MOIs (0.005, 0.025, 0.1, 0.25, 1.0), viral titers were analyzed by a standard TCID 50 assay (left). After infection at an MOI of 0.025, relative expression of viral RNA was analyzed using qRT-PCR at the indicated time points (12, 24, 36, 48, 60 and 72 h). GAPDH mRNA was used as an endogenous control. Data are presented as the mean±SD, n=3. * P

Techniques Used: Infection, Expressing, Quantitative RT-PCR, Western Blot, Staining, In Vitro

41) Product Images from "Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1"

Article Title: Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1500992113

UPAT is required for the tumorigenicity and the expression of RAS-, CDH1-, and hypoxia-related genes in colon cancer cells. ( A ) qRT-PCR analysis of UPAT expression in HCT116 cells infected with a lentivirus harboring an sh UPAT . Results are expressed as
Figure Legend Snippet: UPAT is required for the tumorigenicity and the expression of RAS-, CDH1-, and hypoxia-related genes in colon cancer cells. ( A ) qRT-PCR analysis of UPAT expression in HCT116 cells infected with a lentivirus harboring an sh UPAT . Results are expressed as

Techniques Used: Expressing, Quantitative RT-PCR, Infection

UPAT stabilizes UHRF1 protein by interfering with its ubiquitination and degradation. ( A , Upper ) qRT-PCR analysis of UHRF1 expression in HCT116 cells transfected with siRNA targeting UPAT . Results are expressed as the mean ± SEM ( n = 3). ( A ,
Figure Legend Snippet: UPAT stabilizes UHRF1 protein by interfering with its ubiquitination and degradation. ( A , Upper ) qRT-PCR analysis of UHRF1 expression in HCT116 cells transfected with siRNA targeting UPAT . Results are expressed as the mean ± SEM ( n = 3). ( A ,

Techniques Used: Quantitative RT-PCR, Expressing, Transfection

42) Product Images from "Genome‐wide discovery of tissue‐specific mi RNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis"

Article Title: Genome‐wide discovery of tissue‐specific mi RNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Journal: Plant Biotechnology Journal

doi: 10.1111/pbi.12866

Relative expression analysis of 10 mi RNA s, including nine novel mi RNA s, Ct ‐miR3008a, Ct ‐miR3090, Ct ‐miR3008b, Ct ‐miR3039, Ct ‐miR3016, Ct ‐miR3128, Ct ‐miR3130, Ct ‐miR3135 and Ct ‐miR3157 and one known mi RNA , Ct ‐miR3009 (mi RNA 156), based on qRT ‐ PCR in five different clusterbean tissues.
Figure Legend Snippet: Relative expression analysis of 10 mi RNA s, including nine novel mi RNA s, Ct ‐miR3008a, Ct ‐miR3090, Ct ‐miR3008b, Ct ‐miR3039, Ct ‐miR3016, Ct ‐miR3128, Ct ‐miR3130, Ct ‐miR3135 and Ct ‐miR3157 and one known mi RNA , Ct ‐miR3009 (mi RNA 156), based on qRT ‐ PCR in five different clusterbean tissues.

Techniques Used: Expressing, Quantitative RT-PCR

43) Product Images from "?-catenin promotes the type I IFN synthesis and the IFN-dependent signaling response but is suppressed by influenza A virus-induced RIG-I/NF-?B signaling"

Article Title: ?-catenin promotes the type I IFN synthesis and the IFN-dependent signaling response but is suppressed by influenza A virus-induced RIG-I/NF-?B signaling

Journal: Cell Communication and Signaling : CCS

doi: 10.1186/1478-811X-12-29

The ISG promoter activity is triggered by β- and γ-catenin. (A) A549 cells were transfected with β-catenin and LEF1 for 30 h, and the mRNA level of the type I and type III IFN-dependent MX1 gene was measured by qRT-PCR. The mRNA amount of empty vector-transfected cells was taken as unity. (B and C) Vero cells transfected for 24 h with indicated plasmids were infected with vesicular stomatitis virus (VSV) (MOI = 0.0001) for an additional 24 h. Subsequently, the overexpression of β-catenin was confirmed by immunoblotting of corresponding RIPA lysates (B) and the propagation of VSV by standard plaque titration assay (C) . (D and E) Vero cells were co-transfected with the ISRE luciferase reporter gene and plasmids coding for proteins indicated in column legends. After 24 hours, Vero cells were left unstimulated or treated with 100 U/ml IFN-β for 8 h. The y-axis represents the relative reporter gene activity with luciferase activity of unstimulated, empty vector-transfected cells being set to one. (F) Vero cells were transfected with the ISRE luciferase reporter gene, and its activity in β-catenin- and LEF1-overexpressing cells was measured in the presence or absence of co-transfected p300. The luciferase activity of β-catenin and LEF1-transfected cells was arbitrarily taken as unity. (G) A549 cells were transfected with empty vector or plasmids coding for β-catenin and LEF1 for 30 h, and the interaction of cellular proteins with the DNA was analyzed by ChIP assays using specific antibodies to IRF3 or β-catenin. The co-immunoprecipitated DNA was amplified by qRT-PCR using specific primers for the promoter region of the MX1 gene and is given as the n-fold amount to the IgG control. Representative values from one of three repeated experiments are depicted.
Figure Legend Snippet: The ISG promoter activity is triggered by β- and γ-catenin. (A) A549 cells were transfected with β-catenin and LEF1 for 30 h, and the mRNA level of the type I and type III IFN-dependent MX1 gene was measured by qRT-PCR. The mRNA amount of empty vector-transfected cells was taken as unity. (B and C) Vero cells transfected for 24 h with indicated plasmids were infected with vesicular stomatitis virus (VSV) (MOI = 0.0001) for an additional 24 h. Subsequently, the overexpression of β-catenin was confirmed by immunoblotting of corresponding RIPA lysates (B) and the propagation of VSV by standard plaque titration assay (C) . (D and E) Vero cells were co-transfected with the ISRE luciferase reporter gene and plasmids coding for proteins indicated in column legends. After 24 hours, Vero cells were left unstimulated or treated with 100 U/ml IFN-β for 8 h. The y-axis represents the relative reporter gene activity with luciferase activity of unstimulated, empty vector-transfected cells being set to one. (F) Vero cells were transfected with the ISRE luciferase reporter gene, and its activity in β-catenin- and LEF1-overexpressing cells was measured in the presence or absence of co-transfected p300. The luciferase activity of β-catenin and LEF1-transfected cells was arbitrarily taken as unity. (G) A549 cells were transfected with empty vector or plasmids coding for β-catenin and LEF1 for 30 h, and the interaction of cellular proteins with the DNA was analyzed by ChIP assays using specific antibodies to IRF3 or β-catenin. The co-immunoprecipitated DNA was amplified by qRT-PCR using specific primers for the promoter region of the MX1 gene and is given as the n-fold amount to the IgG control. Representative values from one of three repeated experiments are depicted.

Techniques Used: Activity Assay, Transfection, Quantitative RT-PCR, Plasmid Preparation, Infection, Over Expression, Titration, Luciferase, Chromatin Immunoprecipitation, Immunoprecipitation, Amplification

β-catenin and LEF1 regulate IFN-β promoter activity via IRF-PRD. (A) Vero cells were transfected with the reporter gene plasmid containing the IRF3-responsive elements of the IFN-β enhanceosome along with indicated plasmids, and the reporter gene activity was measured 30 h later. The luciferase activity of β-catenin and LEF1-transfected cells was arbitrarily taken as unity. (B) A549 cells were transfected with empty vector or plasmids coding for β-catenin and LEF1 for 30 h, and the interaction of cellular proteins with the DNA was analyzed by ChIP assays. The amount of amplified DNA in IRF3- and β-catenin-specific immunoprecipitates was quantified by qRT-PCR using primers specific for the promoter region of the IFNB1 gene. Values represent n-folds of IgG controls. One of three independently repeated experiments is depicted as representative.
Figure Legend Snippet: β-catenin and LEF1 regulate IFN-β promoter activity via IRF-PRD. (A) Vero cells were transfected with the reporter gene plasmid containing the IRF3-responsive elements of the IFN-β enhanceosome along with indicated plasmids, and the reporter gene activity was measured 30 h later. The luciferase activity of β-catenin and LEF1-transfected cells was arbitrarily taken as unity. (B) A549 cells were transfected with empty vector or plasmids coding for β-catenin and LEF1 for 30 h, and the interaction of cellular proteins with the DNA was analyzed by ChIP assays. The amount of amplified DNA in IRF3- and β-catenin-specific immunoprecipitates was quantified by qRT-PCR using primers specific for the promoter region of the IFNB1 gene. Values represent n-folds of IgG controls. One of three independently repeated experiments is depicted as representative.

Techniques Used: Activity Assay, Transfection, Plasmid Preparation, Luciferase, Chromatin Immunoprecipitation, Amplification, Quantitative RT-PCR

44) Product Images from "RNA-binding motif protein 47 inhibits Nrf2 activity to suppress tumor growth in lung adenocarcinoma"

Article Title: RNA-binding motif protein 47 inhibits Nrf2 activity to suppress tumor growth in lung adenocarcinoma

Journal: Oncogene

doi: 10.1038/onc.2016.35

Regulation of RBM47 by TGF-β and TTF-1 in lung adenocarcinoma cells. ( a, b ) After the 24-h treatment of A549 cells and H441 cells with 2.5 ng/ml TGF-β, expression levels of RBM47 mRNA and protein were examined by qRT–PCR ( a ) and immunoblot ( b ) analyses, respectively. α-tubulin was used as a loading control in ( b ). Protein expression was quantified using Image J and normalized to that of lane 1 and is indicated below each panel. ( c ) ChIP-seq data of Smad3 and TTF-1 binding at the RBM47 locus in H441 cells. An arrow indicates the transcription starting site of RBM47 . TTF-1 binding ( top panel ) and Smad3 binding ( center and bottom panels ) in TGF-β-treated H441 cells transfected with control or TTF-1 siRNAs, respectively, are shown. ( d ) H441 cells transfected with control or TTF-1 siRNAs were examined by immunoblot analysis to evaluate the effect of TTF-1 on the expression of RBM47 protein. The arrow indicates the endogenous TTF-1 protein. ( e ) A549 cells were transfected with human RBM47 promoter-reporter construct in combination with adenoviral FLAG-TTF-1 or LacZ infection. At 48 h after infection, cells were harvested and assayed for luciferase activities. Averages and standard deviations of the two biological replicates were shown for each condition. Expression of FLAG-TTF-1 was confirmed by immunoblotting ( bottom panel ). ( f ) H441 cells were transfected with human RBM47 promoter-reporter construct in combination with control or TTF-1 siRNAs (siTTF-1#1 and siTTF-1#2). At 48 h after transfection, cells were harvested and assayed for luciferase activities. siCT: control siRNA. Averages and standard deviations of the two biological replicates were shown for each condition. * P
Figure Legend Snippet: Regulation of RBM47 by TGF-β and TTF-1 in lung adenocarcinoma cells. ( a, b ) After the 24-h treatment of A549 cells and H441 cells with 2.5 ng/ml TGF-β, expression levels of RBM47 mRNA and protein were examined by qRT–PCR ( a ) and immunoblot ( b ) analyses, respectively. α-tubulin was used as a loading control in ( b ). Protein expression was quantified using Image J and normalized to that of lane 1 and is indicated below each panel. ( c ) ChIP-seq data of Smad3 and TTF-1 binding at the RBM47 locus in H441 cells. An arrow indicates the transcription starting site of RBM47 . TTF-1 binding ( top panel ) and Smad3 binding ( center and bottom panels ) in TGF-β-treated H441 cells transfected with control or TTF-1 siRNAs, respectively, are shown. ( d ) H441 cells transfected with control or TTF-1 siRNAs were examined by immunoblot analysis to evaluate the effect of TTF-1 on the expression of RBM47 protein. The arrow indicates the endogenous TTF-1 protein. ( e ) A549 cells were transfected with human RBM47 promoter-reporter construct in combination with adenoviral FLAG-TTF-1 or LacZ infection. At 48 h after infection, cells were harvested and assayed for luciferase activities. Averages and standard deviations of the two biological replicates were shown for each condition. Expression of FLAG-TTF-1 was confirmed by immunoblotting ( bottom panel ). ( f ) H441 cells were transfected with human RBM47 promoter-reporter construct in combination with control or TTF-1 siRNAs (siTTF-1#1 and siTTF-1#2). At 48 h after transfection, cells were harvested and assayed for luciferase activities. siCT: control siRNA. Averages and standard deviations of the two biological replicates were shown for each condition. * P

Techniques Used: Expressing, Quantitative RT-PCR, Chromatin Immunoprecipitation, Binding Assay, Transfection, Construct, Infection, Luciferase

RNA-seq and RIP-seq analyses reveal that knockdown of RBM47 elevates Nrf2 activity. ( a ) A549-Luc cells were infected with lentiviral vector encoding control shRNA (shCT) or shRNAs against RBM47 (shRBM47#1 and #2). RBM47 expression was examined in A549-Luc-shCT cells and A549-Luc-shRBM47 cells by immunoblot analysis. ( b ) Enrichment of Nrf2 targets in the list of genes that were upregulated by knockdown of RBM47. Gene expression data obtained by RNA-seq in A549-Luc-shCT cells and A549-Luc-shRBM47#1 cells were used for gene set enrichment analysis. A gene set NFE2L2.V2 of c6 MSigDB oncogenic signature (v4.0) consisting of the direct gene targets of Nrf2 was identified as the second most enriched phenotype of the analysis; its enrichment plot is shown. Normalized enrichment score (NES)=1.854. Expression data of the genes whose expression levels exceeded 10 fragments per kilobases of exon per million sequence read (FPKM) in any of the samples were used for the analysis. ( c ) qRT–PCR analysis of the identified Nrf2 target genes regulated by RBM47. ( d ) RIP-seq data of Nrf2 and its regulatory genes. RIP-seq was performed in A549 cells using anti-RBM47 or normal rabbit IgG (rIgG) and SNRNP70 as a control. RBM47_rep1 and RBM47_rep2 represent biological replicates of anti-RBM47 RIP. Quantified FPKM values of RBM47 RIP samples were normalized against rIgG-RIP-seq FPKM. ( e ) Immunoblotting of KEAP1 and CUL3 proteins in A549-Luc cells expressing shCT or shRBM47s. Protein expression was quantified using Image J and normalized to that of lane 1 and is indicated below each panel. ( f ) qRT–PCR analysis of KEAP1 and CUL3 expression in cells after RBM47 knockdown. ( g ) A quantitative ChIP–PCR analysis of Nrf2 binding at its target-binding regions in A549 cells. HBB : control genomic region. ( h ) qChIP–PCR analysis was performed in H441 cells after knockdown of RBM47 expression by siRNAs (siRBM47#1 and siRBM47#2). siCT: control siRNA. In ( g ) and ( h ), averages and standard deviations of the three technical replicates were shown for each condition. ( i ) Expression of small Maf family and CDKN1A was determined by RNA-seq. Error bars: 95% confidence interval calculated by Cuffdiff.
Figure Legend Snippet: RNA-seq and RIP-seq analyses reveal that knockdown of RBM47 elevates Nrf2 activity. ( a ) A549-Luc cells were infected with lentiviral vector encoding control shRNA (shCT) or shRNAs against RBM47 (shRBM47#1 and #2). RBM47 expression was examined in A549-Luc-shCT cells and A549-Luc-shRBM47 cells by immunoblot analysis. ( b ) Enrichment of Nrf2 targets in the list of genes that were upregulated by knockdown of RBM47. Gene expression data obtained by RNA-seq in A549-Luc-shCT cells and A549-Luc-shRBM47#1 cells were used for gene set enrichment analysis. A gene set NFE2L2.V2 of c6 MSigDB oncogenic signature (v4.0) consisting of the direct gene targets of Nrf2 was identified as the second most enriched phenotype of the analysis; its enrichment plot is shown. Normalized enrichment score (NES)=1.854. Expression data of the genes whose expression levels exceeded 10 fragments per kilobases of exon per million sequence read (FPKM) in any of the samples were used for the analysis. ( c ) qRT–PCR analysis of the identified Nrf2 target genes regulated by RBM47. ( d ) RIP-seq data of Nrf2 and its regulatory genes. RIP-seq was performed in A549 cells using anti-RBM47 or normal rabbit IgG (rIgG) and SNRNP70 as a control. RBM47_rep1 and RBM47_rep2 represent biological replicates of anti-RBM47 RIP. Quantified FPKM values of RBM47 RIP samples were normalized against rIgG-RIP-seq FPKM. ( e ) Immunoblotting of KEAP1 and CUL3 proteins in A549-Luc cells expressing shCT or shRBM47s. Protein expression was quantified using Image J and normalized to that of lane 1 and is indicated below each panel. ( f ) qRT–PCR analysis of KEAP1 and CUL3 expression in cells after RBM47 knockdown. ( g ) A quantitative ChIP–PCR analysis of Nrf2 binding at its target-binding regions in A549 cells. HBB : control genomic region. ( h ) qChIP–PCR analysis was performed in H441 cells after knockdown of RBM47 expression by siRNAs (siRBM47#1 and siRBM47#2). siCT: control siRNA. In ( g ) and ( h ), averages and standard deviations of the three technical replicates were shown for each condition. ( i ) Expression of small Maf family and CDKN1A was determined by RNA-seq. Error bars: 95% confidence interval calculated by Cuffdiff.

Techniques Used: RNA Sequencing Assay, Activity Assay, Infection, Plasmid Preparation, shRNA, Expressing, Sequencing, Quantitative RT-PCR, Chromatin Immunoprecipitation, Polymerase Chain Reaction, Binding Assay

Reduced expression of RBM47 is associated with poor outcomes for lung, breast and gastric cancer patients. ( a ) A scheme of RBM47 protein with interspecies amino acid conservation. RRM1–3, RNA recognition motifs 1–3. ( b ) The subcellular localization of endogenous RBM47 protein after treatment of H441 cells with 2.5 ng/ml TGF-β for 24 h was determined by immunoblotting. ( c ) The levels of RBM47 expression in a panel of 22 cell lines were examined using qRT–PCR and normalized with respect to GAPDH expression. ( d ) Survival rates based on RBM47 expression were analyzed by Kaplan–Meier survival method in lung (overall survival), breast (relapse-free survival) and gastric cancer (overall survival) patients. The half of patients with higher expression of RBM47 mRNA is indicated in red and that with lower expression is indicated in black. A log-rank test was used to compare the variance between the two groups.
Figure Legend Snippet: Reduced expression of RBM47 is associated with poor outcomes for lung, breast and gastric cancer patients. ( a ) A scheme of RBM47 protein with interspecies amino acid conservation. RRM1–3, RNA recognition motifs 1–3. ( b ) The subcellular localization of endogenous RBM47 protein after treatment of H441 cells with 2.5 ng/ml TGF-β for 24 h was determined by immunoblotting. ( c ) The levels of RBM47 expression in a panel of 22 cell lines were examined using qRT–PCR and normalized with respect to GAPDH expression. ( d ) Survival rates based on RBM47 expression were analyzed by Kaplan–Meier survival method in lung (overall survival), breast (relapse-free survival) and gastric cancer (overall survival) patients. The half of patients with higher expression of RBM47 mRNA is indicated in red and that with lower expression is indicated in black. A log-rank test was used to compare the variance between the two groups.

Techniques Used: Expressing, Quantitative RT-PCR

45) Product Images from "Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness"

Article Title: Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness

Journal: BMC Plant Biology

doi: 10.1186/s12870-019-1651-z

qRT-PCR experiments. a Results of the qRT-PCR experiments, shown as expression fold change of ARR and HER relative to CLE at 30 and 126 DPA. Original RNA from peel at 126 DPA and newly extracted from fruitlets at 30 DPA were used. The quantitative analysis confirms the RNA-Seq data for Ciclev10021357 , the SlMADS1 homolog, Ciclev10032572 , Ciclev10021100, Ciclev10020575 and Ciclev10019920 . b Image of ARR, CLE and HER fruitlets at 30 DPA, where the differences in size can be appreciated, the rule on the left side shows mm. Error bars represent SEM values
Figure Legend Snippet: qRT-PCR experiments. a Results of the qRT-PCR experiments, shown as expression fold change of ARR and HER relative to CLE at 30 and 126 DPA. Original RNA from peel at 126 DPA and newly extracted from fruitlets at 30 DPA were used. The quantitative analysis confirms the RNA-Seq data for Ciclev10021357 , the SlMADS1 homolog, Ciclev10032572 , Ciclev10021100, Ciclev10020575 and Ciclev10019920 . b Image of ARR, CLE and HER fruitlets at 30 DPA, where the differences in size can be appreciated, the rule on the left side shows mm. Error bars represent SEM values

Techniques Used: Quantitative RT-PCR, Expressing, RNA Sequencing Assay

46) Product Images from "CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-renewing Somatic Tissue"

Article Title: CSNK1a1 Regulates PRMT1 to Maintain the Progenitor State in Self-renewing Somatic Tissue

Journal: Developmental cell

doi: 10.1016/j.devcel.2017.08.021

CSNK1a1 loss phenocopies PRMT1 loss in epidermal progenitors (A and D) qRT-PCR analysis of CSNK1a1 shRNA knockdown efficiency in primary human keratinocytes. (B and E) Clonogenic assays of human keratinocytes with CSNK1a1 RNAi or control. (C and F) Colonies > 1mm 2 in clonogenic assays are quantified (n=2/group, p
Figure Legend Snippet: CSNK1a1 loss phenocopies PRMT1 loss in epidermal progenitors (A and D) qRT-PCR analysis of CSNK1a1 shRNA knockdown efficiency in primary human keratinocytes. (B and E) Clonogenic assays of human keratinocytes with CSNK1a1 RNAi or control. (C and F) Colonies > 1mm 2 in clonogenic assays are quantified (n=2/group, p

Techniques Used: Quantitative RT-PCR, shRNA

PRMT1 is enriched in progenitors and is required for progenitor maintenance (A) Bar graph representing the mRNA abundance of PRMTs in undifferentiated primary human keratinocytes based on RNA-seq data. X-axis represents reads per kb per million reads (RPKM). (B) Heatmap comparing the relative PRMT mRNA expression levels between undifferentiated and differentiated human keratinocytes based on RNA-seq data. (C) qRT-PCR quantification of relative PRMT1 mRNA expression among undifferentiated state (UD), differentiation day 2 (DF_Day2), and differentiation day 4 (DF_Day4). PRMT1 mRNA is downregulated during keratinocyte differentiation in vitro. (D) Immunoblots demonstrating PRMT1 protein levels decrease during human keratinocyte differentiation. β-tubulin was used as loading control. (E) Immunostaining of PRMT1 in human skin section. PRMT1 protein localizes primarily to nuclei in the basal progenitor epidermal layer [PRMT1=green; collagen VII basement membrane marker=orange; nuclear stain with Hoechst 33342=blue; scale bar=100 microns. Note that rabbit anti-serum tends to cross react with stratum corneum]. (F and I) Immunoblots demonstrating the knockdown efficiency of four independent shRNAs targeting PRMT1 in primary human keratinocytes. (G and J) Clonogenic assays of human keratinocytes with PRMT1 RNAi or control. (H and K) Colonies > 1mm 2 in clonogenic assays are quantified (n=2/group, p
Figure Legend Snippet: PRMT1 is enriched in progenitors and is required for progenitor maintenance (A) Bar graph representing the mRNA abundance of PRMTs in undifferentiated primary human keratinocytes based on RNA-seq data. X-axis represents reads per kb per million reads (RPKM). (B) Heatmap comparing the relative PRMT mRNA expression levels between undifferentiated and differentiated human keratinocytes based on RNA-seq data. (C) qRT-PCR quantification of relative PRMT1 mRNA expression among undifferentiated state (UD), differentiation day 2 (DF_Day2), and differentiation day 4 (DF_Day4). PRMT1 mRNA is downregulated during keratinocyte differentiation in vitro. (D) Immunoblots demonstrating PRMT1 protein levels decrease during human keratinocyte differentiation. β-tubulin was used as loading control. (E) Immunostaining of PRMT1 in human skin section. PRMT1 protein localizes primarily to nuclei in the basal progenitor epidermal layer [PRMT1=green; collagen VII basement membrane marker=orange; nuclear stain with Hoechst 33342=blue; scale bar=100 microns. Note that rabbit anti-serum tends to cross react with stratum corneum]. (F and I) Immunoblots demonstrating the knockdown efficiency of four independent shRNAs targeting PRMT1 in primary human keratinocytes. (G and J) Clonogenic assays of human keratinocytes with PRMT1 RNAi or control. (H and K) Colonies > 1mm 2 in clonogenic assays are quantified (n=2/group, p

Techniques Used: RNA Sequencing Assay, Expressing, Quantitative RT-PCR, In Vitro, Western Blot, Immunostaining, Marker, Staining

47) Product Images from "Genome-wide identification and characterization of the bHLH gene family in tomato"

Article Title: Genome-wide identification and characterization of the bHLH gene family in tomato

Journal: BMC Genomics

doi: 10.1186/s12864-014-1209-2

Expression analyses of the six SlbHLH genes under iron-deficient stress by qRT-PCR. For qRT-PCR, the relative amount of mRNA (y-axis) was calculated by according to the description in Methods. The x-axis indicates the shoot (S) and root (R) of tomato under iron-sufficient (+Fe) and iron deficient (-Fe) conditions.
Figure Legend Snippet: Expression analyses of the six SlbHLH genes under iron-deficient stress by qRT-PCR. For qRT-PCR, the relative amount of mRNA (y-axis) was calculated by according to the description in Methods. The x-axis indicates the shoot (S) and root (R) of tomato under iron-sufficient (+Fe) and iron deficient (-Fe) conditions.

Techniques Used: Expressing, Quantitative RT-PCR

48) Product Images from "TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species"

Article Title: TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species

Journal: Mobile DNA

doi: 10.1186/s13100-017-0098-8

Time-course expression levels of active AACA elements in Pyrus bretschneideri . The positions of the primers used for transcriptional validation are indicated in the schematic of each element in qRT-PCR region. The expression levels were detected in the fruit flesh of four developmental stages, pollen, stylet, leaf and pericarp. a–c , leaves under cold ( d–f ), heat ( g–i ), and salt ( j–l ) treatments for PbrAACA1_IT5 ( a, d, g, j ), PbrAACA4_IT11 ( b, e, h, k ) and PbrAACA4_IT14 ( c, f, i, l ). Error bars indicate the standard deviations of three biological replicates
Figure Legend Snippet: Time-course expression levels of active AACA elements in Pyrus bretschneideri . The positions of the primers used for transcriptional validation are indicated in the schematic of each element in qRT-PCR region. The expression levels were detected in the fruit flesh of four developmental stages, pollen, stylet, leaf and pericarp. a–c , leaves under cold ( d–f ), heat ( g–i ), and salt ( j–l ) treatments for PbrAACA1_IT5 ( a, d, g, j ), PbrAACA4_IT11 ( b, e, h, k ) and PbrAACA4_IT14 ( c, f, i, l ). Error bars indicate the standard deviations of three biological replicates

Techniques Used: Expressing, Quantitative RT-PCR

49) Product Images from "ASBEL–TCF3 complex is required for the tumorigenicity of colorectal cancer cells"

Article Title: ASBEL–TCF3 complex is required for the tumorigenicity of colorectal cancer cells

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1605938113

Negative feedback regulation of the expression of ASBEL by ATF3 in colon cancer cells. ( A ) qRT-PCR analysis of ASBEL expression in HCT116 cells transfected with siRNA targeting ATF3. Results are expressed as the mean ± SD ( n = 3). * P
Figure Legend Snippet: Negative feedback regulation of the expression of ASBEL by ATF3 in colon cancer cells. ( A ) qRT-PCR analysis of ASBEL expression in HCT116 cells transfected with siRNA targeting ATF3. Results are expressed as the mean ± SD ( n = 3). * P

Techniques Used: Expressing, Quantitative RT-PCR, Transfection

TCF3 is associated with ASBEL and is required for the proliferation of colon cancer cells. ( A ) qRT-PCR analysis of ASBEL expression in HCT116, HT29, and DLD-1 cells infected with a lentivirus harboring an shRNA targeting ASBEL . Results are expressed as the mean ± SD ( n = 3). * P
Figure Legend Snippet: TCF3 is associated with ASBEL and is required for the proliferation of colon cancer cells. ( A ) qRT-PCR analysis of ASBEL expression in HCT116, HT29, and DLD-1 cells infected with a lentivirus harboring an shRNA targeting ASBEL . Results are expressed as the mean ± SD ( n = 3). * P

Techniques Used: Quantitative RT-PCR, Expressing, Infection, shRNA

ATF3 expression is required for the tumorigenicity of colon cancer cells. ( A ) qRT-PCR analysis of ATF3 expression in HCT116 cells infected with a lentivirus harboring an shRNA targeting ATF3. Results are expressed as the mean ± SD ( n = 2). * P
Figure Legend Snippet: ATF3 expression is required for the tumorigenicity of colon cancer cells. ( A ) qRT-PCR analysis of ATF3 expression in HCT116 cells infected with a lentivirus harboring an shRNA targeting ATF3. Results are expressed as the mean ± SD ( n = 2). * P

Techniques Used: Expressing, Quantitative RT-PCR, Infection, shRNA

Transactivation of ASBEL and TCF3 by β-catenin is required for β-catenin–mediated proliferation of colon cancer cells. ( A ) Depiction of a screen to identify β-catenin target genes. ( B ) qRT-PCR analysis of the expression of the indicated genes in DLD-1 cells transfected with an siRNA targeting β-catenin or a control siRNA (siCont). Two distinct siRNAs targeting β-catenin (siβ-catenin #1 and #2) were used. Results are expressed as the mean ± SD ( n = 3). * P
Figure Legend Snippet: Transactivation of ASBEL and TCF3 by β-catenin is required for β-catenin–mediated proliferation of colon cancer cells. ( A ) Depiction of a screen to identify β-catenin target genes. ( B ) qRT-PCR analysis of the expression of the indicated genes in DLD-1 cells transfected with an siRNA targeting β-catenin or a control siRNA (siCont). Two distinct siRNAs targeting β-catenin (siβ-catenin #1 and #2) were used. Results are expressed as the mean ± SD ( n = 3). * P

Techniques Used: Quantitative RT-PCR, Expressing, Transfection

50) Product Images from "A20 plays a critical role in the immunoregulatory function of mesenchymal stem cells"

Article Title: A20 plays a critical role in the immunoregulatory function of mesenchymal stem cells

Journal: Journal of Cellular and Molecular Medicine

doi: 10.1111/jcmm.12849

Proliferation and differentiation capacities of sh CTRL C3 MSC s and shA20 C3 MSC s. ( A ) BrdU incorporation coupled with 7 AAD staining was analysed by flow cytometry. C3 MSC s were cultured in ( B ) osteogenic or ( C ) adipogenic differentiation medium for 14 days, and stained with ALP (bar = 100 μm) or Oil Red O (bar = 50 μm). ( D ) C3 MSC s cultured in osteogenic or adipogenic medium for the indicated times were analysed for ALP , Osterix, PPAR ‐γ and aP 2 by qRT ‐ PCR , ** P
Figure Legend Snippet: Proliferation and differentiation capacities of sh CTRL C3 MSC s and shA20 C3 MSC s. ( A ) BrdU incorporation coupled with 7 AAD staining was analysed by flow cytometry. C3 MSC s were cultured in ( B ) osteogenic or ( C ) adipogenic differentiation medium for 14 days, and stained with ALP (bar = 100 μm) or Oil Red O (bar = 50 μm). ( D ) C3 MSC s cultured in osteogenic or adipogenic medium for the indicated times were analysed for ALP , Osterix, PPAR ‐γ and aP 2 by qRT ‐ PCR , ** P

Techniques Used: BrdU Incorporation Assay, Staining, Flow Cytometry, Cytometry, Cell Culture, ALP Assay, Quantitative RT-PCR

Morphological and phenotypic characterization of C3 MSC s after A20 knockdown. ( A ) qRT ‐ PCR analysis of A20 mRNA levels with or without A20 knockdown. ( B ) Morphology and ( C ) size of cultured sh CTRL C3 MSC s and shA20 C3 MSC s were analysed by microscopy and flow cytometry. ( D ) Cell surface markers were analysed by flow cytometry, ** P
Figure Legend Snippet: Morphological and phenotypic characterization of C3 MSC s after A20 knockdown. ( A ) qRT ‐ PCR analysis of A20 mRNA levels with or without A20 knockdown. ( B ) Morphology and ( C ) size of cultured sh CTRL C3 MSC s and shA20 C3 MSC s were analysed by microscopy and flow cytometry. ( D ) Cell surface markers were analysed by flow cytometry, ** P

Techniques Used: Quantitative RT-PCR, Cell Culture, Microscopy, Flow Cytometry, Cytometry

Inflammatory cytokines induce A20 expression in MSC s. MSC s ( A ) and C3H/10T1/2 ( B and C ) were treated with 0, 2, 5 and 10 ng/ml IFN ‐γ and TNF ‐α for 24 hrs. A20 mRNA and protein levels were examined by qRT ‐ PCR and Western blot analysis. MSC s ( D ) and C3H/10T1/2 ( E and F ) were treated with 5 ng/ml IFN ‐γ and TNF ‐α for 0, 6, 12 and 24 hrs, and mRNA and protein expression levels were determined by qRT ‐ PCR and Western blot analysis, respectively.
Figure Legend Snippet: Inflammatory cytokines induce A20 expression in MSC s. MSC s ( A ) and C3H/10T1/2 ( B and C ) were treated with 0, 2, 5 and 10 ng/ml IFN ‐γ and TNF ‐α for 24 hrs. A20 mRNA and protein levels were examined by qRT ‐ PCR and Western blot analysis. MSC s ( D ) and C3H/10T1/2 ( E and F ) were treated with 5 ng/ml IFN ‐γ and TNF ‐α for 0, 6, 12 and 24 hrs, and mRNA and protein expression levels were determined by qRT ‐ PCR and Western blot analysis, respectively.

Techniques Used: Expressing, Quantitative RT-PCR, Western Blot

A20 inhibits TNF ‐α and promotes IL ‐10 production in C3 MSC s, and the p38/ MAPK pathway is involved in A20‐induced immunomodulation. TNF ‐α ( A ) and IL ‐10 ( B , left) expression was examined with or without stimulation with 5 ng/ml IFN ‐γ and TNF ‐α by qRT ‐ PCR . IL ‐10 protein level was determined by ELISA ( B , right). ( C ) The time courses of p38 phosphorylation in response to 5 ng/ml IFN ‐γ and TNF ‐α was determined by immunoblotting, ** P
Figure Legend Snippet: A20 inhibits TNF ‐α and promotes IL ‐10 production in C3 MSC s, and the p38/ MAPK pathway is involved in A20‐induced immunomodulation. TNF ‐α ( A ) and IL ‐10 ( B , left) expression was examined with or without stimulation with 5 ng/ml IFN ‐γ and TNF ‐α by qRT ‐ PCR . IL ‐10 protein level was determined by ELISA ( B , right). ( C ) The time courses of p38 phosphorylation in response to 5 ng/ml IFN ‐γ and TNF ‐α was determined by immunoblotting, ** P

Techniques Used: Expressing, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

51) Product Images from "MiR-497∼195 cluster regulates angiogenesis during coupling with osteogenesis by maintaining endothelial Notch and HIF-1α activity"

Article Title: MiR-497∼195 cluster regulates angiogenesis during coupling with osteogenesis by maintaining endothelial Notch and HIF-1α activity

Journal: Nature Communications

doi: 10.1038/ncomms16003

MiR-497∼195 cluster targets Fbxw7 and P4HTM to maintain endothelial Notch and HIF-α activity. ( a , b ) qRT-PCR analysis of the relative levels of miR-195 ( a ) and miR-497 ( b ) expression in BMECs transfected with agomiR-497∼195, antagomiR-497∼195 or their negative controls. NC, negative control. ( c , d ) qRT-PCR analysis of the relative levels of CD31 ( c ) and Emcn ( d ) mRNA expression in endothelial cells. ( e – i ) Western blot analysis ( e ) and the quantitation of the relative levels of NICD ( f ), HIFα ( g ), Fbxw7 ( h ) and P4HTM ( i ) protein expression in BMECs transfected with agomiR-497∼195, antagomiR-497∼195 or control. ( n =3 in each group from three independent experiments). ( j , k ) ECs were transfected with luciferase reporter carrying WT or MUT 3′-UTR of the Fbxw7 or P4HTM gene, WT-pGL3-Fbxw7 or MUT-pGL3-Fbxw7 ( j ) WT-pGL3-P4HTM and MUT-pGL3-P4HTM ( k ) respectively, and cotransfected with agomiR-497∼195 or agomiR-NC. Effects of miR-497∼195 on the reporter constructs were determined at 48 h after transfection. Firefly luciferase values, normalized for renilla luciferase, are presented. ( n =3 in each group from three independent experiments). ( l , m ) Western blot analysis ( l ) and the quantitation ( m ) of the relative levels of Fbxw7, NICD protein expression in BMECs transfected with Fbxw7 siRNA or control. ( n , o ) Western blot analysis ( n ) and the quantitation ( o ) of the relative levels of P4HTM, HIFα protein expression in BMECs transfected with P4HTM siRNA or control. ( n =3 in each group from three independent experiments). Data shown as mean±s.d. * P
Figure Legend Snippet: MiR-497∼195 cluster targets Fbxw7 and P4HTM to maintain endothelial Notch and HIF-α activity. ( a , b ) qRT-PCR analysis of the relative levels of miR-195 ( a ) and miR-497 ( b ) expression in BMECs transfected with agomiR-497∼195, antagomiR-497∼195 or their negative controls. NC, negative control. ( c , d ) qRT-PCR analysis of the relative levels of CD31 ( c ) and Emcn ( d ) mRNA expression in endothelial cells. ( e – i ) Western blot analysis ( e ) and the quantitation of the relative levels of NICD ( f ), HIFα ( g ), Fbxw7 ( h ) and P4HTM ( i ) protein expression in BMECs transfected with agomiR-497∼195, antagomiR-497∼195 or control. ( n =3 in each group from three independent experiments). ( j , k ) ECs were transfected with luciferase reporter carrying WT or MUT 3′-UTR of the Fbxw7 or P4HTM gene, WT-pGL3-Fbxw7 or MUT-pGL3-Fbxw7 ( j ) WT-pGL3-P4HTM and MUT-pGL3-P4HTM ( k ) respectively, and cotransfected with agomiR-497∼195 or agomiR-NC. Effects of miR-497∼195 on the reporter constructs were determined at 48 h after transfection. Firefly luciferase values, normalized for renilla luciferase, are presented. ( n =3 in each group from three independent experiments). ( l , m ) Western blot analysis ( l ) and the quantitation ( m ) of the relative levels of Fbxw7, NICD protein expression in BMECs transfected with Fbxw7 siRNA or control. ( n , o ) Western blot analysis ( n ) and the quantitation ( o ) of the relative levels of P4HTM, HIFα protein expression in BMECs transfected with P4HTM siRNA or control. ( n =3 in each group from three independent experiments). Data shown as mean±s.d. * P

Techniques Used: Activity Assay, Quantitative RT-PCR, Expressing, Transfection, Negative Control, Western Blot, Quantitation Assay, Luciferase, Construct

MiR-497∼195 cluster was strongly expressed in CD31 hi Emcn hi endothelial cells. ( a ) Microarray profiling results of deregulated miRNAs in CD31 hi Emcn hi and CD31 lo Emcn lo endothelial cells (Type H ECs and Type L ECs). ( n =3 per group). ( b ) qRT-PCR analysis of miR-195/miR-497 level in Type H ECs and Type L ECs. ( n =5 in each group from three independent experiments). ( c , d ) qRT-PCR analysis of the levels of miR-195 ( c ) and miR-497 ( d ) expression in endothelial cells derived from the mice at different ages. ( n =5 mice in each group from three independent experiments). ( e , f ) Age-associated changes of miR-195 ( e ) and miR-497 ( f ) levels in endothelial cells from 33 human females. Data shown as mean±s.d. * P
Figure Legend Snippet: MiR-497∼195 cluster was strongly expressed in CD31 hi Emcn hi endothelial cells. ( a ) Microarray profiling results of deregulated miRNAs in CD31 hi Emcn hi and CD31 lo Emcn lo endothelial cells (Type H ECs and Type L ECs). ( n =3 per group). ( b ) qRT-PCR analysis of miR-195/miR-497 level in Type H ECs and Type L ECs. ( n =5 in each group from three independent experiments). ( c , d ) qRT-PCR analysis of the levels of miR-195 ( c ) and miR-497 ( d ) expression in endothelial cells derived from the mice at different ages. ( n =5 mice in each group from three independent experiments). ( e , f ) Age-associated changes of miR-195 ( e ) and miR-497 ( f ) levels in endothelial cells from 33 human females. Data shown as mean±s.d. * P

Techniques Used: Microarray, Quantitative RT-PCR, Expressing, Derivative Assay, Mouse Assay

52) Product Images from "The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis"

Article Title: The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1617903113

MCL-mediated uptake of cancer cells by Kupffer cells and suppression of liver metastasis. ( A ) Expression levels of Mcl , Dectin-1 , and Mincle mRNAs in hepatocytes and Kupffer cells were analyzed by qRT-PCR. ( B and C ) SL4 cells (2 × 10 5 cells) were
Figure Legend Snippet: MCL-mediated uptake of cancer cells by Kupffer cells and suppression of liver metastasis. ( A ) Expression levels of Mcl , Dectin-1 , and Mincle mRNAs in hepatocytes and Kupffer cells were analyzed by qRT-PCR. ( B and C ) SL4 cells (2 × 10 5 cells) were

Techniques Used: Expressing, Quantitative RT-PCR

53) Product Images from "Cytotoxic Effect of Recombinant Mycobacterium tuberculosis CFP-10/ESAT-6 Protein on the Crucial Pathways of WI-38 Cells"

Article Title: Cytotoxic Effect of Recombinant Mycobacterium tuberculosis CFP-10/ESAT-6 Protein on the Crucial Pathways of WI-38 Cells

Journal: Journal of Biomedicine and Biotechnology

doi: 10.1155/2009/917084

Validation of microarray data by qRT-PCR analysis for 5 genes: (a) LAMA4, (b) ITGB1, (c) PIK3R3, (d) BIRC3, and (e) NFKBIA. The data are expressed as mean values (± standard deviation) of three experiments.
Figure Legend Snippet: Validation of microarray data by qRT-PCR analysis for 5 genes: (a) LAMA4, (b) ITGB1, (c) PIK3R3, (d) BIRC3, and (e) NFKBIA. The data are expressed as mean values (± standard deviation) of three experiments.

Techniques Used: Microarray, Quantitative RT-PCR, Standard Deviation

54) Product Images from "Endogenous CHRNA7-ligand SLURP1 as a potential tumor suppressor and anti-nicotinic factor in pancreatic cancer"

Article Title: Endogenous CHRNA7-ligand SLURP1 as a potential tumor suppressor and anti-nicotinic factor in pancreatic cancer

Journal: Oncotarget

doi: 10.18632/oncotarget.24312

CHRNA7 is a major binding site for SLURP1 on PDAC cells ( A ) Simultaneous FACS and qRT-PCR analyses revealed CHRNA7-positivity of all eight tested PDAC cell lines, whereby membranous CHRNA7-staining showed significant inter-experimental variability and lack of correlation with RNA levels. The graph summarizes the data of two independent experiments shown below and measuring CHRNA7 mRNA (qRT-PCR; log10-transformed number of transcripts/10k PPIB) and surface protein expression (log10-transformed mean fluorescence intensity/MFI values) in unrelated passages of each cell line. ( B ) Individual FACS histograms illustrating intra- and inter-experimental variability are shown as an overlap of anti-CHRNA7-IgG (gray tinted area) and rabbit IgG (bold black line; isotype control) profiles; the difference in their geometric MFIs was used to calculate final MFI value for each culture. ( C ) qRT-PCR data demonstrating the inter-experimental stability of CHRNA7 mRNA expression also revealed the existence of the two groups, whereby CHRNA7 high -group but not CHRNA7 neg/low -group showed RNA-agreeable, stable pattern of protein expression. ( D – F ) The siRNA-based depletion of CHRNA7 confirmed the specificity of the reagents such as primers (qRT-PCR, D) and antibodies (Western blot, E, and FACS, F). As illustrated for COLO357 cultures, transfection with three commercially available CHRNA7-specific siRNA sets (si#1, si#2, si#3) eliminated over 75% of CHRNA7 mRNA and protein compared to the transfection of cells with negative control siRNA set (neg.si) or left untreated (control). ( G ) siRNA-based depletion of CHRNA7 indicated the preferential binding of SLURP1 to this receptor on PDAC cells. For comparison, FITC-conjugated SLURP1 was added to COLO357 and PANC-1 cells transfected with three different CHRNA7-siRNA sets (‘CHRNA7-depletion’ group depicted by grey-, green- and rose-colored profiles for si#1, si#2 and si#3, respectively) and to cells remaining intact or transfected with negative siRNA (‘controls’ group depicted by blue and lilac-colored profiles).
Figure Legend Snippet: CHRNA7 is a major binding site for SLURP1 on PDAC cells ( A ) Simultaneous FACS and qRT-PCR analyses revealed CHRNA7-positivity of all eight tested PDAC cell lines, whereby membranous CHRNA7-staining showed significant inter-experimental variability and lack of correlation with RNA levels. The graph summarizes the data of two independent experiments shown below and measuring CHRNA7 mRNA (qRT-PCR; log10-transformed number of transcripts/10k PPIB) and surface protein expression (log10-transformed mean fluorescence intensity/MFI values) in unrelated passages of each cell line. ( B ) Individual FACS histograms illustrating intra- and inter-experimental variability are shown as an overlap of anti-CHRNA7-IgG (gray tinted area) and rabbit IgG (bold black line; isotype control) profiles; the difference in their geometric MFIs was used to calculate final MFI value for each culture. ( C ) qRT-PCR data demonstrating the inter-experimental stability of CHRNA7 mRNA expression also revealed the existence of the two groups, whereby CHRNA7 high -group but not CHRNA7 neg/low -group showed RNA-agreeable, stable pattern of protein expression. ( D – F ) The siRNA-based depletion of CHRNA7 confirmed the specificity of the reagents such as primers (qRT-PCR, D) and antibodies (Western blot, E, and FACS, F). As illustrated for COLO357 cultures, transfection with three commercially available CHRNA7-specific siRNA sets (si#1, si#2, si#3) eliminated over 75% of CHRNA7 mRNA and protein compared to the transfection of cells with negative control siRNA set (neg.si) or left untreated (control). ( G ) siRNA-based depletion of CHRNA7 indicated the preferential binding of SLURP1 to this receptor on PDAC cells. For comparison, FITC-conjugated SLURP1 was added to COLO357 and PANC-1 cells transfected with three different CHRNA7-siRNA sets (‘CHRNA7-depletion’ group depicted by grey-, green- and rose-colored profiles for si#1, si#2 and si#3, respectively) and to cells remaining intact or transfected with negative siRNA (‘controls’ group depicted by blue and lilac-colored profiles).

Techniques Used: Binding Assay, FACS, Quantitative RT-PCR, Staining, Transformation Assay, Expressing, Fluorescence, Western Blot, Transfection, Negative Control

Preservation of CHRNA7 expression in the pancreas is associated with better prognosis for operable PDAC patients ( A ) CHRNA7 mRNA expression was determined by qRT-PCR in 66 pancreatic samples obtained from the organ donors and patients with chronic pancreatitis (CP) or pancreatic adenocarcinoma (PDAC). The groups were compared using the Kruskal-Wallis test ( p = 0.004) with Dunn’s procedure, which established significant down-regulation of CHRNA7 in PDAC patients ( p
Figure Legend Snippet: Preservation of CHRNA7 expression in the pancreas is associated with better prognosis for operable PDAC patients ( A ) CHRNA7 mRNA expression was determined by qRT-PCR in 66 pancreatic samples obtained from the organ donors and patients with chronic pancreatitis (CP) or pancreatic adenocarcinoma (PDAC). The groups were compared using the Kruskal-Wallis test ( p = 0.004) with Dunn’s procedure, which established significant down-regulation of CHRNA7 in PDAC patients ( p

Techniques Used: Preserving, Expressing, Quantitative RT-PCR

55) Product Images from "CPEB1 modulates differentiation of glioma stem cells via downregulation of HES1 and SIRT1 expression"

Article Title: CPEB1 modulates differentiation of glioma stem cells via downregulation of HES1 and SIRT1 expression

Journal: Oncotarget

doi:

CPEB1 regulates translation of HES1 and SIRT1 mRNAs (A and B) WB of CPEB1, SIRT1 and HES1 in CSC2 (A) and X01 (B) with serum or without serum. (C and D) WB of CPEB1, SIRT1 and HES1 in CSC2 infected with CPEB1-expressing lentiviral or control construct (C) and infected with shCPEB1-expressing lentiviral or control construct (D). Expression level of SIRT1 and HES1 proteins were quantified with ImageJ software. Each protein level was normalized with that of β-Actin (loading control). (E and F) qRT-PCR of SIRT1 and HES1 in CSC2 infected with CPEB1-expressing lentiviral or control construct (E) and infected with shCPEB1-expressing lentiviral or control construct (F).
Figure Legend Snippet: CPEB1 regulates translation of HES1 and SIRT1 mRNAs (A and B) WB of CPEB1, SIRT1 and HES1 in CSC2 (A) and X01 (B) with serum or without serum. (C and D) WB of CPEB1, SIRT1 and HES1 in CSC2 infected with CPEB1-expressing lentiviral or control construct (C) and infected with shCPEB1-expressing lentiviral or control construct (D). Expression level of SIRT1 and HES1 proteins were quantified with ImageJ software. Each protein level was normalized with that of β-Actin (loading control). (E and F) qRT-PCR of SIRT1 and HES1 in CSC2 infected with CPEB1-expressing lentiviral or control construct (E) and infected with shCPEB1-expressing lentiviral or control construct (F).

Techniques Used: Western Blot, Infection, Expressing, Construct, Software, Quantitative RT-PCR

56) Product Images from "Gene Expression Patterns Analysis in the Supraspinatus Muscle after a Rotator Cuff Tear in a Mouse Model"

Article Title: Gene Expression Patterns Analysis in the Supraspinatus Muscle after a Rotator Cuff Tear in a Mouse Model

Journal: BioMed Research International

doi: 10.1155/2018/5859013

Validation of microarray gene expression patterns using qRT-PCR analysis. (a) Cdk1, (b) keratin 8, (c) keratin 18, (d) myogenin, (e) myostatin, and (f) actn3.
Figure Legend Snippet: Validation of microarray gene expression patterns using qRT-PCR analysis. (a) Cdk1, (b) keratin 8, (c) keratin 18, (d) myogenin, (e) myostatin, and (f) actn3.

Techniques Used: Microarray, Expressing, Quantitative RT-PCR

57) Product Images from "Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle"

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle

Journal: Reproductive Biology and Endocrinology : RB & E

doi: 10.1186/s12958-015-0010-7

Graphs of gene expression profiles showing a significant difference. Twelve genes measured by qRT-PCR in the growing (white box; n = 7), plateau (grey box; n = 7) and atretic (black box; n = 6) follicles had significantly different expression levels (p-value
Figure Legend Snippet: Graphs of gene expression profiles showing a significant difference. Twelve genes measured by qRT-PCR in the growing (white box; n = 7), plateau (grey box; n = 7) and atretic (black box; n = 6) follicles had significantly different expression levels (p-value

Techniques Used: Expressing, Quantitative RT-PCR, Significance Assay

58) Product Images from "Genome-, Transcriptome- and Proteome-Wide Analyses of the Gliadin Gene Families in Triticum urartu"

Article Title: Genome-, Transcriptome- and Proteome-Wide Analyses of the Gliadin Gene Families in Triticum urartu

Journal: PLoS ONE

doi: 10.1371/journal.pone.0131559

Expression patterns of the T . urartu gliadin genes as shown by RNA-Seq and qRT-PCR. (A) The expression levels (RPKM values) calculated from the RNA-Seq data. (B) The normalized expression levels, as determined using qRT-PCR.
Figure Legend Snippet: Expression patterns of the T . urartu gliadin genes as shown by RNA-Seq and qRT-PCR. (A) The expression levels (RPKM values) calculated from the RNA-Seq data. (B) The normalized expression levels, as determined using qRT-PCR.

Techniques Used: Expressing, RNA Sequencing Assay, Quantitative RT-PCR

59) Product Images from "Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice"

Article Title: Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice

Journal: PLoS ONE

doi: 10.1371/journal.pone.0140675

qRT-PCR analysis of the relative expression of miRNAs and targets. A) Comparison of miRNAs (fold changes) between illumina reads and qRT-PCR between control and salt-treated library. B) Relative expression of miRNAs and their targets under control and salinity stress condition. The data represents the mean values ± SD of three replicates.
Figure Legend Snippet: qRT-PCR analysis of the relative expression of miRNAs and targets. A) Comparison of miRNAs (fold changes) between illumina reads and qRT-PCR between control and salt-treated library. B) Relative expression of miRNAs and their targets under control and salinity stress condition. The data represents the mean values ± SD of three replicates.

Techniques Used: Quantitative RT-PCR, Expressing

60) Product Images from "Transposon insertion sequencing reveals T4SS as the major genetic trait for conjugation transfer of multi-drug resistance pEIB202 from Edwardsiella"

Article Title: Transposon insertion sequencing reveals T4SS as the major genetic trait for conjugation transfer of multi-drug resistance pEIB202 from Edwardsiella

Journal: BMC Microbiology

doi: 10.1186/s12866-017-1013-7

Antibiotics inhibit the expression of T4SS but does not affect the copy number of pEIB202. a Copy number of pEIB202 in WT grown with or without antibiotics at their sublethal concentrations or in ∆ esrB measured by qPCR. b qRT-PCR analysis of the expression of T4SS genes in WT grown with or without antibiotics at their sublethal concentrations (1/4 of MIC). * P
Figure Legend Snippet: Antibiotics inhibit the expression of T4SS but does not affect the copy number of pEIB202. a Copy number of pEIB202 in WT grown with or without antibiotics at their sublethal concentrations or in ∆ esrB measured by qPCR. b qRT-PCR analysis of the expression of T4SS genes in WT grown with or without antibiotics at their sublethal concentrations (1/4 of MIC). * P

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR

TIS identification and verification of genes associated with pEIB202 transfer. a Artemis screenshot of abundance of reads in topA , p007 and T4SS genes in input ( red ) and output ( green ) samples. The height of the red and green bars correlates with the number of reads. b The transfer frequency of pEIB202 from each strain to ∆P::pNQ705K. Strains were conjugated at 30 °C for 8 h. c qRT-PCR analysis of the expression of T4SS genes in each strain grown in LB. * P
Figure Legend Snippet: TIS identification and verification of genes associated with pEIB202 transfer. a Artemis screenshot of abundance of reads in topA , p007 and T4SS genes in input ( red ) and output ( green ) samples. The height of the red and green bars correlates with the number of reads. b The transfer frequency of pEIB202 from each strain to ∆P::pNQ705K. Strains were conjugated at 30 °C for 8 h. c qRT-PCR analysis of the expression of T4SS genes in each strain grown in LB. * P

Techniques Used: Quantitative RT-PCR, Expressing

61) Product Images from "Overexpression of Histone Deacetylase 6 Enhances Resistance to Porcine Reproductive and Respiratory Syndrome Virus in Pigs"

Article Title: Overexpression of Histone Deacetylase 6 Enhances Resistance to Porcine Reproductive and Respiratory Syndrome Virus in Pigs

Journal: PLoS ONE

doi: 10.1371/journal.pone.0169317

Production and identification of F0 TG pigs. (A) Schematic diagram of the transgenic vector (pCMV-pHDAC6-Puro). The pair of black arrows indicates the primers used to identify the transgenic insert in TG pigs and in fibroblast colonies. The pair of green arrows indicates the primers used to identify exogenous HDAC6 mRNA in pigs. The pair of red arrows indicates the primers used to determine total HDAC6 mRNA levels in F1 pigs. (B) PCR assay to detect founder transgenic pigs. The PCR product (771 bp) was the GFP tag of the inserted transgene, which was amplified using the HDAC6-F/R primer pair. M, 100 bp DNA ladder; Lanes 1–9, founders No. 1–9; w, water; P, plasmid control; N, wild-type pig genomic DNA, used as the negative control. (C) qRT-PCR analysis of exogenous HDAC6 expression in different tissues (blood, liver, kidney, skin, lung, intestine and spleen) of the F0 transgenic pig using the Q-GFP-F/R primer pair. The blood sample data are presented as the mean±SD from 3 individuals (No. 1, 2 and 3). The data from other tissues are presented as the mean±SD from 3 repeated experiments. RNA from the intestines was used as the reference sample. WT, wild-type control. (D) Western blot analysis of F0 transgenic pigs. The samples were collected from tissues of TG (No.1) and WT pigs. The protein samples were probed with an anti-GFP antibody.
Figure Legend Snippet: Production and identification of F0 TG pigs. (A) Schematic diagram of the transgenic vector (pCMV-pHDAC6-Puro). The pair of black arrows indicates the primers used to identify the transgenic insert in TG pigs and in fibroblast colonies. The pair of green arrows indicates the primers used to identify exogenous HDAC6 mRNA in pigs. The pair of red arrows indicates the primers used to determine total HDAC6 mRNA levels in F1 pigs. (B) PCR assay to detect founder transgenic pigs. The PCR product (771 bp) was the GFP tag of the inserted transgene, which was amplified using the HDAC6-F/R primer pair. M, 100 bp DNA ladder; Lanes 1–9, founders No. 1–9; w, water; P, plasmid control; N, wild-type pig genomic DNA, used as the negative control. (C) qRT-PCR analysis of exogenous HDAC6 expression in different tissues (blood, liver, kidney, skin, lung, intestine and spleen) of the F0 transgenic pig using the Q-GFP-F/R primer pair. The blood sample data are presented as the mean±SD from 3 individuals (No. 1, 2 and 3). The data from other tissues are presented as the mean±SD from 3 repeated experiments. RNA from the intestines was used as the reference sample. WT, wild-type control. (D) Western blot analysis of F0 transgenic pigs. The samples were collected from tissues of TG (No.1) and WT pigs. The protein samples were probed with an anti-GFP antibody.

Techniques Used: Transgenic Assay, Plasmid Preparation, Polymerase Chain Reaction, Amplification, Negative Control, Quantitative RT-PCR, Expressing, Western Blot

HDAC6 Overexpression inhibits viral gene expression and PRRSV production in PAMs. (A) qRT-PCR analysis of HDAC6 expression in PAMs isolated from pigs using the Q-HDAC6-F/R primer pair. HDAC6 expression is presented as a ratio relative to the level of GAPDH . The data are presented as the mean±SD from three independent experiments. (B) Western blot analysis of PAMs isolated from F1 pigs. The protein samples were probed with anti-Actub and GAPDH antibodies. (C) qRT-PCR analysis of viral ORF7 RNA levels in TG and NTG PAMs that were inoculated with the PRRSV strain CH-1a (MOI = 0.5) for 24, 48 and 72 h. The data represent the results of three independent experiments (mean±SD). (D) qRT-PCR analysis of viral ORF7 RNA levels in TG and NTG PAMs that were inoculated with the PRRSV strain JXA1 (MOI = 0.25) for 24 and 48 h. The data are presented relative to the expression of GAPDH mRNA and represent the results of three independent experiments (mean±SD). RNA from NTG PAMs at 24 hpi was used as the reference sample. Statistical significance was analyzed using a t-test. *, P
Figure Legend Snippet: HDAC6 Overexpression inhibits viral gene expression and PRRSV production in PAMs. (A) qRT-PCR analysis of HDAC6 expression in PAMs isolated from pigs using the Q-HDAC6-F/R primer pair. HDAC6 expression is presented as a ratio relative to the level of GAPDH . The data are presented as the mean±SD from three independent experiments. (B) Western blot analysis of PAMs isolated from F1 pigs. The protein samples were probed with anti-Actub and GAPDH antibodies. (C) qRT-PCR analysis of viral ORF7 RNA levels in TG and NTG PAMs that were inoculated with the PRRSV strain CH-1a (MOI = 0.5) for 24, 48 and 72 h. The data represent the results of three independent experiments (mean±SD). (D) qRT-PCR analysis of viral ORF7 RNA levels in TG and NTG PAMs that were inoculated with the PRRSV strain JXA1 (MOI = 0.25) for 24 and 48 h. The data are presented relative to the expression of GAPDH mRNA and represent the results of three independent experiments (mean±SD). RNA from NTG PAMs at 24 hpi was used as the reference sample. Statistical significance was analyzed using a t-test. *, P

Techniques Used: Over Expression, Expressing, Quantitative RT-PCR, Isolation, Western Blot

Determination of HDAC6 expression in F1 generation transgenic pigs. (A) qRT-PCR analysis of exogenous HDAC6 expression in the lungs and skin of F1 TG (n = 9) and sibling NTG pigs (lung, n = 10; skin, n = 6) using the Q-GFP-F/R primer pair. The data are presented as the mean ± SD. The relative expression of GFP was calculated using the 2 -Δct method. (B) qRT-PCR analysis of HDAC6 expression in lungs of F1 TG (n = 9) and sibling NTG pigs (n = 10) using the Q-HDAC6-F/R primer pair. (C) qRT-PCR analysis of HDAC6 expression in the skin of F1 TG (n = 9) and sibling NTG pigs (n = 6) using the Q-HDAC6-F/R primer pair. The data are presented as the mean±SD. The mRNA relative expression of total HDAC6 was calculated using the 2 -ΔΔct method (RNA from NTG pigs was used as the reference sample). GAPDH was used as an internal qRT-PCR control. Statistical significance was analyzed using a t-test. ***, P
Figure Legend Snippet: Determination of HDAC6 expression in F1 generation transgenic pigs. (A) qRT-PCR analysis of exogenous HDAC6 expression in the lungs and skin of F1 TG (n = 9) and sibling NTG pigs (lung, n = 10; skin, n = 6) using the Q-GFP-F/R primer pair. The data are presented as the mean ± SD. The relative expression of GFP was calculated using the 2 -Δct method. (B) qRT-PCR analysis of HDAC6 expression in lungs of F1 TG (n = 9) and sibling NTG pigs (n = 10) using the Q-HDAC6-F/R primer pair. (C) qRT-PCR analysis of HDAC6 expression in the skin of F1 TG (n = 9) and sibling NTG pigs (n = 6) using the Q-HDAC6-F/R primer pair. The data are presented as the mean±SD. The mRNA relative expression of total HDAC6 was calculated using the 2 -ΔΔct method (RNA from NTG pigs was used as the reference sample). GAPDH was used as an internal qRT-PCR control. Statistical significance was analyzed using a t-test. ***, P

Techniques Used: Expressing, Transgenic Assay, Quantitative RT-PCR

62) Product Images from "Generation of Pigs Resistant to Highly Pathogenic-Porcine Reproductive and Respiratory Syndrome Virus through Gene Editing of CD163"

Article Title: Generation of Pigs Resistant to Highly Pathogenic-Porcine Reproductive and Respiratory Syndrome Virus through Gene Editing of CD163

Journal: International Journal of Biological Sciences

doi: 10.7150/ijbs.25862

CD163 Mut/Mut PAMs are remarkably resistant to HP-PRRSV infection . (A) After infection with the HP-PRRSV strain JXwn06 at the indicated MOIs (0.005, 0.025, 0.1, 0.25, 2.0), culture supernatants were collected at 36 hpi, and viral titers were analyzed by a standard TCID 50 assay (left). Cells were collected to measure relative expression of viral RNA by qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (B) After infection with HP-PRRSV strain JXwn06 at an MOI of 0.1, viral titers were measured by TCID 50 at the indicated time points (12, 24, 36 and 48 h) (left). Relative expression of viral RNA was analyzed using qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (C) PAMs were infected with JXwn06 at an MOI of 0.1, and 36 h later, levels of PRRSV protein GP5 were analyzed by Western blotting analysis (left). Expression of α-tubulin was shown as a loading control. After 48 h, cells were fixed for detection of PRRSV N protein (Green) by immunofluorescent staining(right). The nuclei (blue) were stained with DAPI. (D) The in vitro infection experiment was carried out with the HP-PRRSV strain WUH3. At the indicated MOIs (0.005, 0.025, 0.1, 0.25, 1.0), viral titers were analyzed by a standard TCID 50 assay (left). After infection at an MOI of 0.025, relative expression of viral RNA was analyzed using qRT-PCR at the indicated time points (12, 24, 36, 48, 60 and 72 h). GAPDH mRNA was used as an endogenous control. Data are presented as the mean±SD, n=3. * P
Figure Legend Snippet: CD163 Mut/Mut PAMs are remarkably resistant to HP-PRRSV infection . (A) After infection with the HP-PRRSV strain JXwn06 at the indicated MOIs (0.005, 0.025, 0.1, 0.25, 2.0), culture supernatants were collected at 36 hpi, and viral titers were analyzed by a standard TCID 50 assay (left). Cells were collected to measure relative expression of viral RNA by qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (B) After infection with HP-PRRSV strain JXwn06 at an MOI of 0.1, viral titers were measured by TCID 50 at the indicated time points (12, 24, 36 and 48 h) (left). Relative expression of viral RNA was analyzed using qRT-PCR (right). GAPDH mRNA was used as an endogenous control. (C) PAMs were infected with JXwn06 at an MOI of 0.1, and 36 h later, levels of PRRSV protein GP5 were analyzed by Western blotting analysis (left). Expression of α-tubulin was shown as a loading control. After 48 h, cells were fixed for detection of PRRSV N protein (Green) by immunofluorescent staining(right). The nuclei (blue) were stained with DAPI. (D) The in vitro infection experiment was carried out with the HP-PRRSV strain WUH3. At the indicated MOIs (0.005, 0.025, 0.1, 0.25, 1.0), viral titers were analyzed by a standard TCID 50 assay (left). After infection at an MOI of 0.025, relative expression of viral RNA was analyzed using qRT-PCR at the indicated time points (12, 24, 36, 48, 60 and 72 h). GAPDH mRNA was used as an endogenous control. Data are presented as the mean±SD, n=3. * P

Techniques Used: Infection, Expressing, Quantitative RT-PCR, Western Blot, Staining, In Vitro

63) Product Images from "Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells"

Article Title: Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells

Journal: Oncogene

doi: 10.1038/s41388-018-0144-0

Role of Nestin in highly malignant pancreatic cancer cell lines. a Expression of NES mRNA in the cell lines derived from human pancreatic cancer cell lines was determined by qRT-PCR analysis. b , c Expression of Nestin protein in the cell lines derived from SUIT-2 cells ( b ) and Panc-1 cells ( c ) was determined by immunoblotting. d Expression of Nestin protein in parental SUIT-2 and SUIT-2-3P#2 cells was determined by immunocytochemistry. Enlarged pictures of the middle panels are also shown in the right panels. Scale bars are 100 µm. e Expression of Nestin in SUIT-2-3P#2 cells upon treatment with control or Nestin siRNAs. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, the expression of Nestin protein was determined by immunoblotting. f Cell proliferation assay of the SUIT-2-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. g Expression of Nestin in Panc-1-3P#2 cells. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, expression of Nestin protein was determined by immunoblotting. h Survival of the Panc-1-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. Data are presented as mean (duplicate; a ) and mean ± SD ( f , h ), respectively. * P
Figure Legend Snippet: Role of Nestin in highly malignant pancreatic cancer cell lines. a Expression of NES mRNA in the cell lines derived from human pancreatic cancer cell lines was determined by qRT-PCR analysis. b , c Expression of Nestin protein in the cell lines derived from SUIT-2 cells ( b ) and Panc-1 cells ( c ) was determined by immunoblotting. d Expression of Nestin protein in parental SUIT-2 and SUIT-2-3P#2 cells was determined by immunocytochemistry. Enlarged pictures of the middle panels are also shown in the right panels. Scale bars are 100 µm. e Expression of Nestin in SUIT-2-3P#2 cells upon treatment with control or Nestin siRNAs. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, the expression of Nestin protein was determined by immunoblotting. f Cell proliferation assay of the SUIT-2-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. g Expression of Nestin in Panc-1-3P#2 cells. Cells were transfected with control siRNA or siRNAs targeting Nestin. Forty-eight hours after transfection, expression of Nestin protein was determined by immunoblotting. h Survival of the Panc-1-3P#2 cells. Cell number was counted 6 d after the transfection of siRNAs. Representative images (left) and the number of living cells (right) are shown. Scale bars are 200 µm. Data are presented as mean (duplicate; a ) and mean ± SD ( f , h ), respectively. * P

Techniques Used: Expressing, Derivative Assay, Quantitative RT-PCR, Immunocytochemistry, Transfection, Proliferation Assay

Mechanisms of acquisition of the malignant phenotype in vivo. a Morphological features of clones isolated from parental SUIT-2 cells. Scale bars are 50 µm. b , c Expression of E-cadherin in the clones from SUIT-2 cells. Expression of CDH1 mRNA and that of E-cadherin protein were determined by qRT-PCR analysis ( b ) and immunoblotting ( c ), respectively. d Tumor-forming ability of the clones isolated from SUIT-2 cells. An equal number of each clone from parental SUIT-2 cells was inoculated into the pancreas. One month after inoculation, the primary tumor was excised (left) and tumor weight was measured (right). e Morphological features of the 3P cells from each clone. The clone-3P cells were established from each clone with three cycles of orthotopic inoculation. Representative images are shown. Scale bars are 50 µm. f Expression levels of E-cadherin, MMP2, and Nestin in the SUIT-2 clones and 3P clones were determined by qRT-PCR analysis. Data are presented as mean (duplicate; b , f ) and mean ± SD ( d ), respectively. **** P
Figure Legend Snippet: Mechanisms of acquisition of the malignant phenotype in vivo. a Morphological features of clones isolated from parental SUIT-2 cells. Scale bars are 50 µm. b , c Expression of E-cadherin in the clones from SUIT-2 cells. Expression of CDH1 mRNA and that of E-cadherin protein were determined by qRT-PCR analysis ( b ) and immunoblotting ( c ), respectively. d Tumor-forming ability of the clones isolated from SUIT-2 cells. An equal number of each clone from parental SUIT-2 cells was inoculated into the pancreas. One month after inoculation, the primary tumor was excised (left) and tumor weight was measured (right). e Morphological features of the 3P cells from each clone. The clone-3P cells were established from each clone with three cycles of orthotopic inoculation. Representative images are shown. Scale bars are 50 µm. f Expression levels of E-cadherin, MMP2, and Nestin in the SUIT-2 clones and 3P clones were determined by qRT-PCR analysis. Data are presented as mean (duplicate; b , f ) and mean ± SD ( d ), respectively. **** P

Techniques Used: In Vivo, Clone Assay, Isolation, Expressing, Quantitative RT-PCR

Gene expression profiles of pancreatic cancer cell lines. a Gene expression profiles of the cells lines derived from SUIT-2 cells using RNA-seq analysis. The result of the cluster analysis is shown by a dendrogram. b Number of upregulated and downregulated genes (left and right, respectively). The genes were purified as follows: upregulated genes: the fragments per kilobase of exon per million mapped sequence reads (FPKM) in SUIT-2-3P cells or SUIT-2-3sc cells were > 3 and increased more than threefold, compared to the FPKM in parental SUIT-2; downregulated genes: the FPKM in parental SUIT-2 were > 3 and decreased more than twofold, compared to the FPKM in SUIT-2-3P cells or SUIT-2-3sc cells. c Gene ontology analysis of upregulated genes in ( b ). Biological processes activated in both SUIT-2-3P and SUIT-2-3sc cells (top) and specifically in SUIT-2-3P cells (bottom) are shown. P -values for comparison between parental SUIT-2 and SUIT-2-3P cells are shown. d Gene expression profiles of the cell lines derived from Panc-1 cells obtained by RNA-seq analyses. The result of the cluster analysis is shown by a dendrogram. e Gene ontology analysis of upregulated genes in Panc-1 cells. Biological processes activated in Panc-1-3P cells are shown. P -values for comparison between parental Panc-1 and Panc-1-3P cells are shown. f Three patterns for upregulation of gene expression in each cancer cell line. Expression levels of MMP2 , ABCG2 , and KRT5 mRNA were determined by qRT-PCR analysis. Data are presented as mean (duplicate; f )
Figure Legend Snippet: Gene expression profiles of pancreatic cancer cell lines. a Gene expression profiles of the cells lines derived from SUIT-2 cells using RNA-seq analysis. The result of the cluster analysis is shown by a dendrogram. b Number of upregulated and downregulated genes (left and right, respectively). The genes were purified as follows: upregulated genes: the fragments per kilobase of exon per million mapped sequence reads (FPKM) in SUIT-2-3P cells or SUIT-2-3sc cells were > 3 and increased more than threefold, compared to the FPKM in parental SUIT-2; downregulated genes: the FPKM in parental SUIT-2 were > 3 and decreased more than twofold, compared to the FPKM in SUIT-2-3P cells or SUIT-2-3sc cells. c Gene ontology analysis of upregulated genes in ( b ). Biological processes activated in both SUIT-2-3P and SUIT-2-3sc cells (top) and specifically in SUIT-2-3P cells (bottom) are shown. P -values for comparison between parental SUIT-2 and SUIT-2-3P cells are shown. d Gene expression profiles of the cell lines derived from Panc-1 cells obtained by RNA-seq analyses. The result of the cluster analysis is shown by a dendrogram. e Gene ontology analysis of upregulated genes in Panc-1 cells. Biological processes activated in Panc-1-3P cells are shown. P -values for comparison between parental Panc-1 and Panc-1-3P cells are shown. f Three patterns for upregulation of gene expression in each cancer cell line. Expression levels of MMP2 , ABCG2 , and KRT5 mRNA were determined by qRT-PCR analysis. Data are presented as mean (duplicate; f )

Techniques Used: Expressing, Derivative Assay, RNA Sequencing Assay, Purification, Sequencing, Quantitative RT-PCR

Characterization of highly malignant cancer cell lines derived from SUIT-2 cells. a Cell proliferation assay of the cell lines derived from SUIT-2 cells. Cells were seeded into 96-well plates and cultured for 2–4 d. Relative absorbance (450–595 nm) at the indicated days is shown. b Morphological features of the cell lines derived from SUIT-2 cells. Scale bars are 50 µm. c , d Expression of E-cadherin in the cell lines derived from SUIT-2 cells. Expression levels of CDH1 mRNA and amounts of E-cadherin protein were determined by qRT-PCR analysis ( c ) and immunoblotting ( d ), respectively. e Adhesion assay of the cell lines derived from SUIT-2 cells. Cells were seeded into fibronectin-coated 96-well plates under the FBS-free conditions and cultured for 30 min. The images of adhered cells (left) and the absorbance at 570 nm (right) are shown. f Chamber migration assay of the cell lines derived from SUIT-2 cells. Cells were seeded into the chamber and incubated for 24 h. The representative images (left) and the number of migrated cells (right) are shown. Scale bars are 100 µm. Data are presented as mean (duplicate; c ) and mean ± SD ( e , f ), respectively. ** P
Figure Legend Snippet: Characterization of highly malignant cancer cell lines derived from SUIT-2 cells. a Cell proliferation assay of the cell lines derived from SUIT-2 cells. Cells were seeded into 96-well plates and cultured for 2–4 d. Relative absorbance (450–595 nm) at the indicated days is shown. b Morphological features of the cell lines derived from SUIT-2 cells. Scale bars are 50 µm. c , d Expression of E-cadherin in the cell lines derived from SUIT-2 cells. Expression levels of CDH1 mRNA and amounts of E-cadherin protein were determined by qRT-PCR analysis ( c ) and immunoblotting ( d ), respectively. e Adhesion assay of the cell lines derived from SUIT-2 cells. Cells were seeded into fibronectin-coated 96-well plates under the FBS-free conditions and cultured for 30 min. The images of adhered cells (left) and the absorbance at 570 nm (right) are shown. f Chamber migration assay of the cell lines derived from SUIT-2 cells. Cells were seeded into the chamber and incubated for 24 h. The representative images (left) and the number of migrated cells (right) are shown. Scale bars are 100 µm. Data are presented as mean (duplicate; c ) and mean ± SD ( e , f ), respectively. ** P

Techniques Used: Derivative Assay, Proliferation Assay, Cell Culture, Expressing, Quantitative RT-PCR, Cell Adhesion Assay, Migration, Incubation

64) Product Images from "Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture"

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

Journal: BMC Plant Biology

doi: 10.1186/s12870-018-1545-5

Expression profile of GhGH3s based on RNA-seq and qRT-PCR in various tissue/organs/stages. a Trends in GhGH3 gene expression based on publicly available RNA-seq data. Expression of individual genes are shown for 20 GhGH3s . Numbers on the x-axis indicate days post anthesis, with negative numbers implying days before anthesis. The prefix OV is for ovules and F for fiber. Green, black and red backgrounds represent low, intermediate and high expression levels, respectively. The original RPKM (reads per kilobase per million) values are normalized to 0–1 and shown in boxes. b Pattern of gene expression by qRT-PCR analysis. Expression of allele pairs or individual genes are shown. Values on the y-axis represent relative expression levels while the x-axis indicates days post anthesis. Materials from the field under normal conditions were tagged and sampled. The relative expression levels of GhGH3 genes were measured in roots (R), stems (S), leaves (L), flowers (FL), early stage developing ovules with attached fibers (1, 3, 5 DPA OF, ovules plus fibers), and different stages of detached ovules and fibers (7, 10, 15, 20 DPA O/F, ovules or fibers). GhHis 3 was used as an internal control to normalize the expression data. Error bars show standard deviation calculated from three replicates
Figure Legend Snippet: Expression profile of GhGH3s based on RNA-seq and qRT-PCR in various tissue/organs/stages. a Trends in GhGH3 gene expression based on publicly available RNA-seq data. Expression of individual genes are shown for 20 GhGH3s . Numbers on the x-axis indicate days post anthesis, with negative numbers implying days before anthesis. The prefix OV is for ovules and F for fiber. Green, black and red backgrounds represent low, intermediate and high expression levels, respectively. The original RPKM (reads per kilobase per million) values are normalized to 0–1 and shown in boxes. b Pattern of gene expression by qRT-PCR analysis. Expression of allele pairs or individual genes are shown. Values on the y-axis represent relative expression levels while the x-axis indicates days post anthesis. Materials from the field under normal conditions were tagged and sampled. The relative expression levels of GhGH3 genes were measured in roots (R), stems (S), leaves (L), flowers (FL), early stage developing ovules with attached fibers (1, 3, 5 DPA OF, ovules plus fibers), and different stages of detached ovules and fibers (7, 10, 15, 20 DPA O/F, ovules or fibers). GhHis 3 was used as an internal control to normalize the expression data. Error bars show standard deviation calculated from three replicates

Techniques Used: Expressing, RNA Sequencing Assay, Quantitative RT-PCR, Standard Deviation

Organization of regulatory elements of GhGH3s and their expression in response to phytohormones. a The regulatory region of each GhGH3 gene was analyzed, the numbers indicate the sum of various cis -acting elements response to the same stimuli. b The summary of GhGH3 expression response to treatment with IAA, SA, BL and GA in roots (R) and stems (S). Each orthologous pair from At- and Dt-subgenome of G. hirsutum was designed as a single gene and tested together due to their highly identical sequences. In total, 11 analogue genes standing for 20 GhGH3s were generated and could be divided into 3 subgroups (subgroups 1–3). The expression pattern of 11 analogue genes was detected by qRT-PCR. The relative expression intensity, that is, the ratio of the highest expression level to that of the 0 h control, was allocated into six different grades ranging from suppression shown as black boxes to over 20-fold induction shown as red boxes
Figure Legend Snippet: Organization of regulatory elements of GhGH3s and their expression in response to phytohormones. a The regulatory region of each GhGH3 gene was analyzed, the numbers indicate the sum of various cis -acting elements response to the same stimuli. b The summary of GhGH3 expression response to treatment with IAA, SA, BL and GA in roots (R) and stems (S). Each orthologous pair from At- and Dt-subgenome of G. hirsutum was designed as a single gene and tested together due to their highly identical sequences. In total, 11 analogue genes standing for 20 GhGH3s were generated and could be divided into 3 subgroups (subgroups 1–3). The expression pattern of 11 analogue genes was detected by qRT-PCR. The relative expression intensity, that is, the ratio of the highest expression level to that of the 0 h control, was allocated into six different grades ranging from suppression shown as black boxes to over 20-fold induction shown as red boxes

Techniques Used: Expressing, Generated, Quantitative RT-PCR

65) Product Images from "Assessment of the Effects of Bisphenol A on Dopamine Synthesis and Blood Vessels in the Goldfish Brain"

Article Title: Assessment of the Effects of Bisphenol A on Dopamine Synthesis and Blood Vessels in the Goldfish Brain

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms20246206

DEGs in the fluid shear stress and atherosclerosis pathway and validation by qRT-PCR. ( A ) Expression levels of 6 DEGs in the fluid shear stress and atherosclerosis pathway from the transcriptome data. ( B ) Validation of DEGs in the fluid shear stress and atherosclerosis pathway by qRT-PCR ( n = 3). CG: Control group; TG: BPA treatment group; and FPKM: Fragments per kilobase of transcript per million mapped reads. The qRT-PCR results were calculated from at least three independent experiments. EF1 was used as an internal normalization control. The data are expressed as the mean ± SD (* p
Figure Legend Snippet: DEGs in the fluid shear stress and atherosclerosis pathway and validation by qRT-PCR. ( A ) Expression levels of 6 DEGs in the fluid shear stress and atherosclerosis pathway from the transcriptome data. ( B ) Validation of DEGs in the fluid shear stress and atherosclerosis pathway by qRT-PCR ( n = 3). CG: Control group; TG: BPA treatment group; and FPKM: Fragments per kilobase of transcript per million mapped reads. The qRT-PCR results were calculated from at least three independent experiments. EF1 was used as an internal normalization control. The data are expressed as the mean ± SD (* p

Techniques Used: Quantitative RT-PCR, Expressing

DEGs in the dopaminergic signaling pathway and analysis of the expression of dopaminergic signaling pathway-related genes by qRT-PCR. ( A ) Expression levels of 3 DEGs in the dopaminergic signaling pathway from the transcriptome data. ( B ) Expression levels of 6 dopaminergic signaling pathway-related genes determined by qRT-PCR ( n = 3). CG: Control group; TG: BPA treatment group; and FPKM: Fragments per kilobase of transcript per million mapped reads. The qRT-PCR results were calculated from at least three independent experiments. EF1 was used as an internal normalization control. The data are expressed as the mean ± SD (* p
Figure Legend Snippet: DEGs in the dopaminergic signaling pathway and analysis of the expression of dopaminergic signaling pathway-related genes by qRT-PCR. ( A ) Expression levels of 3 DEGs in the dopaminergic signaling pathway from the transcriptome data. ( B ) Expression levels of 6 dopaminergic signaling pathway-related genes determined by qRT-PCR ( n = 3). CG: Control group; TG: BPA treatment group; and FPKM: Fragments per kilobase of transcript per million mapped reads. The qRT-PCR results were calculated from at least three independent experiments. EF1 was used as an internal normalization control. The data are expressed as the mean ± SD (* p

Techniques Used: Expressing, Quantitative RT-PCR

66) Product Images from "Association of doublecortin-like kinase 1 with tumor aggressiveness and poor biochemical recurrence-free survival in prostate cancer"

Article Title: Association of doublecortin-like kinase 1 with tumor aggressiveness and poor biochemical recurrence-free survival in prostate cancer

Journal: OncoTargets and therapy

doi: 10.2147/OTT.S157295

qRT-PCR and Western blot analysis of DCLK1 expression in fresh PCa (n=25) and BPH (n=25) tissues. Notes: ( A ) Relative DCLK1 mRNA level was significantly higher in PCa tissues compared with BPH. Horizontal lines represent mean with SD. ( B ) Relative protein expression level of DCLK1/GAPDH detected by Western blot was markedly increased in PCa tissues. ( C ) Representative Western blot of DCLK1 protein in five paired PCa (C) and BPH (N) tissues. Data are presented as the mean ± SD; *** P
Figure Legend Snippet: qRT-PCR and Western blot analysis of DCLK1 expression in fresh PCa (n=25) and BPH (n=25) tissues. Notes: ( A ) Relative DCLK1 mRNA level was significantly higher in PCa tissues compared with BPH. Horizontal lines represent mean with SD. ( B ) Relative protein expression level of DCLK1/GAPDH detected by Western blot was markedly increased in PCa tissues. ( C ) Representative Western blot of DCLK1 protein in five paired PCa (C) and BPH (N) tissues. Data are presented as the mean ± SD; *** P

Techniques Used: Quantitative RT-PCR, Western Blot, Expressing

qRT-PCR and Western blot analysis of DCLK1 expression in PCa cell lines. Notes: ( A and B ) Relative DCLK1 mRNA and protein expression levels were markedly increased in PCa cell lines (LNCaP, PC3, DU145, and 22Rv1) compared with the normal epithelial cell RWPE-1. ( C ) Representative Western blot of DCLK1 protein in cell lines. Data are presented as the mean ± SD; * P
Figure Legend Snippet: qRT-PCR and Western blot analysis of DCLK1 expression in PCa cell lines. Notes: ( A and B ) Relative DCLK1 mRNA and protein expression levels were markedly increased in PCa cell lines (LNCaP, PC3, DU145, and 22Rv1) compared with the normal epithelial cell RWPE-1. ( C ) Representative Western blot of DCLK1 protein in cell lines. Data are presented as the mean ± SD; * P

Techniques Used: Quantitative RT-PCR, Western Blot, Expressing

67) Product Images from "Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1"

Article Title: Long noncoding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1500992113

UPAT is required for the tumorigenicity and the expression of RAS-, CDH1-, and hypoxia-related genes in colon cancer cells. ( A ) qRT-PCR analysis of UPAT expression in HCT116 cells infected with a lentivirus harboring an sh UPAT . Results are expressed as
Figure Legend Snippet: UPAT is required for the tumorigenicity and the expression of RAS-, CDH1-, and hypoxia-related genes in colon cancer cells. ( A ) qRT-PCR analysis of UPAT expression in HCT116 cells infected with a lentivirus harboring an sh UPAT . Results are expressed as

Techniques Used: Expressing, Quantitative RT-PCR, Infection

UPAT stabilizes UHRF1 protein by interfering with its ubiquitination and degradation. ( A , Upper ) qRT-PCR analysis of UHRF1 expression in HCT116 cells transfected with siRNA targeting UPAT . Results are expressed as the mean ± SEM ( n = 3). ( A ,
Figure Legend Snippet: UPAT stabilizes UHRF1 protein by interfering with its ubiquitination and degradation. ( A , Upper ) qRT-PCR analysis of UHRF1 expression in HCT116 cells transfected with siRNA targeting UPAT . Results are expressed as the mean ± SEM ( n = 3). ( A ,

Techniques Used: Quantitative RT-PCR, Expressing, Transfection

68) Product Images from "Quantitative Proteomics Identify Novel miR-155 Target Proteins"

Article Title: Quantitative Proteomics Identify Novel miR-155 Target Proteins

Journal: PLoS ONE

doi: 10.1371/journal.pone.0022146

Western blot analysis and qRT-PCR analysis of five selected target proteins. The protein levels A or mRNA levels B of the miR-155 overexpression (HEK293T pCMX miR-155) are compared to the control (HEK293T pCMX empty). The values of the controls are set to 1. The standard bars show the standard deviation between the four A or three B biological replicates. *: Student's t-test
Figure Legend Snippet: Western blot analysis and qRT-PCR analysis of five selected target proteins. The protein levels A or mRNA levels B of the miR-155 overexpression (HEK293T pCMX miR-155) are compared to the control (HEK293T pCMX empty). The values of the controls are set to 1. The standard bars show the standard deviation between the four A or three B biological replicates. *: Student's t-test

Techniques Used: Western Blot, Quantitative RT-PCR, Over Expression, Standard Deviation

69) Product Images from "NLRP6, decreased in gastric cancer, suppresses tumorigenicity of gastric cancer cells"

Article Title: NLRP6, decreased in gastric cancer, suppresses tumorigenicity of gastric cancer cells

Journal: Cancer Management and Research

doi: 10.2147/CMAR.S182980

Effects of NLRP6 on STAT3 signaling. Notes: ( A ) Immunoblot of phosphorylated STAT3, STAT3, Bcl-2, and MMP-2. Blots are representative of three separate experiments. ( B ) mRNA levels of Bcl-2 and MMP-2 were assessed by qRT-PCR. ( C ) BGC-823 and HGC-27 cells were transfected with a Bcl-2 or an MMP-2 luciferase reporter plasmid. The cells were then cultured for 48 hours before determination of normalized luciferase activity. WT, wild-type cells; vector, cells stably expressed control vector; NLR6, cells stably expressed NLRP6. *** P
Figure Legend Snippet: Effects of NLRP6 on STAT3 signaling. Notes: ( A ) Immunoblot of phosphorylated STAT3, STAT3, Bcl-2, and MMP-2. Blots are representative of three separate experiments. ( B ) mRNA levels of Bcl-2 and MMP-2 were assessed by qRT-PCR. ( C ) BGC-823 and HGC-27 cells were transfected with a Bcl-2 or an MMP-2 luciferase reporter plasmid. The cells were then cultured for 48 hours before determination of normalized luciferase activity. WT, wild-type cells; vector, cells stably expressed control vector; NLR6, cells stably expressed NLRP6. *** P

Techniques Used: Quantitative RT-PCR, Transfection, Luciferase, Plasmid Preparation, Cell Culture, Activity Assay, Stable Transfection

70) Product Images from "Genetic Control of Lithium Sensitivity and Regulation of Inositol Biosynthetic Genes"

Article Title: Genetic Control of Lithium Sensitivity and Regulation of Inositol Biosynthetic Genes

Journal: PLoS ONE

doi: 10.1371/journal.pone.0011151

PO regulates gene expression. A , Expression of ino1 in wild type, dpoA null cells and wild type cells following overnight treatment with 1.2 mM Z-pro-L-prolinal (PO inhibitor), measured by Northern analysis. rnlA expression was used as a loading control. The graph shows the expression of ino1 quantified on a phosphoimager (Biorad) and normalised to rnlA relative to wild type or DMSO carrier treated controls (mean ± standard error of 3 independent experiments). B , The expression of genes involved in inositol metabolism ( Table S1 ). Gene expression in wild type cells following overnight treatment with Z-pro-L-prolinal or the equivalent amount of DMSO carrier, and dpoA null mutant cells was measured by qRT-PCR, and normalised to rnlA expression levels. Values plotted are relative to the carrier control cells (mean ± standard error of 3 independent experiments). * P
Figure Legend Snippet: PO regulates gene expression. A , Expression of ino1 in wild type, dpoA null cells and wild type cells following overnight treatment with 1.2 mM Z-pro-L-prolinal (PO inhibitor), measured by Northern analysis. rnlA expression was used as a loading control. The graph shows the expression of ino1 quantified on a phosphoimager (Biorad) and normalised to rnlA relative to wild type or DMSO carrier treated controls (mean ± standard error of 3 independent experiments). B , The expression of genes involved in inositol metabolism ( Table S1 ). Gene expression in wild type cells following overnight treatment with Z-pro-L-prolinal or the equivalent amount of DMSO carrier, and dpoA null mutant cells was measured by qRT-PCR, and normalised to rnlA expression levels. Values plotted are relative to the carrier control cells (mean ± standard error of 3 independent experiments). * P

Techniques Used: Expressing, Northern Blot, Mutagenesis, Quantitative RT-PCR

PO regulates expression of human IMPA1, IMPA2 and ISYNA1 genes. A , A diagram to illustrate the gene regulatory network through which PO activity regulates expression of the IMPA1, IMPA2 and ISYNA1 genes. The gene regulatory network is separate from ligand-stimulated regulation of IP 3 signalling via phospholipase C (PLC), but interacts via changes in gene expression or interchange of soluble IP 3 . * marks genes and enzyme activities associated with bipolar mood disorder. B , HEK293 cells were treated with either mipp1 specific or non-targetting siRNA for 24 hours with or without 130 µM Z-pro-L-prolinal (PO inhibitor). Gene expression was quantified by qRT-PCR using expression of B2M as a reference. Expression of IMPA1, IMPA2 and ISYNA1 genes was quantified as percentage relative change compared to control (DMSO carrier treated, non-targeted siRNA samples). * p
Figure Legend Snippet: PO regulates expression of human IMPA1, IMPA2 and ISYNA1 genes. A , A diagram to illustrate the gene regulatory network through which PO activity regulates expression of the IMPA1, IMPA2 and ISYNA1 genes. The gene regulatory network is separate from ligand-stimulated regulation of IP 3 signalling via phospholipase C (PLC), but interacts via changes in gene expression or interchange of soluble IP 3 . * marks genes and enzyme activities associated with bipolar mood disorder. B , HEK293 cells were treated with either mipp1 specific or non-targetting siRNA for 24 hours with or without 130 µM Z-pro-L-prolinal (PO inhibitor). Gene expression was quantified by qRT-PCR using expression of B2M as a reference. Expression of IMPA1, IMPA2 and ISYNA1 genes was quantified as percentage relative change compared to control (DMSO carrier treated, non-targeted siRNA samples). * p

Techniques Used: Expressing, Activity Assay, Planar Chromatography, Quantitative RT-PCR

71) Product Images from "DOCK1 Regulates Growth and Motility through the RRP1B-Claudin-1 Pathway in Claudin-Low Breast Cancer Cells"

Article Title: DOCK1 Regulates Growth and Motility through the RRP1B-Claudin-1 Pathway in Claudin-Low Breast Cancer Cells

Journal: Cancers

doi: 10.3390/cancers11111762

Depletion of DOCK1 transcriptionally upregulates the CLDN and tight-junction protein gene expression. ( A , B ) Claudin-low breast cancer cells were treated with shDOCK1 for three days. Collected cells were used for gene expression analysis by qRT-PCR analysis. The levels shown by qRT-PCR analysis were normalized to the level of β-actin ( ACTB ) and were expressed as the mean ± SE of three independent experiments. * p
Figure Legend Snippet: Depletion of DOCK1 transcriptionally upregulates the CLDN and tight-junction protein gene expression. ( A , B ) Claudin-low breast cancer cells were treated with shDOCK1 for three days. Collected cells were used for gene expression analysis by qRT-PCR analysis. The levels shown by qRT-PCR analysis were normalized to the level of β-actin ( ACTB ) and were expressed as the mean ± SE of three independent experiments. * p

Techniques Used: Expressing, Quantitative RT-PCR

72) Product Images from "Comparison of Developmental and Stress-Induced Nodule Senescence in Medicago truncatula 1 1 [C] 1 [C] [W] 1 [C] [W] [OA]"

Article Title: Comparison of Developmental and Stress-Induced Nodule Senescence in Medicago truncatula 1 1 [C] 1 [C] [W] 1 [C] [W] [OA]

Journal: Plant Physiology

doi: 10.1104/pp.109.151399

Comparison of developmental and dark-induced nodule senescence by qRT-PCR analysis of developmental nodule senescence marker genes. The expression profiles of 58 genes that were up-regulated during developmental nodule senescence were analyzed during
Figure Legend Snippet: Comparison of developmental and dark-induced nodule senescence by qRT-PCR analysis of developmental nodule senescence marker genes. The expression profiles of 58 genes that were up-regulated during developmental nodule senescence were analyzed during

Techniques Used: Quantitative RT-PCR, Marker, Expressing

73) Product Images from "Long-Distance RNA-RNA Interactions in the Coronavirus Genome Form High-Order Structures Promoting Discontinuous RNA Synthesis during Transcription"

Article Title: Long-Distance RNA-RNA Interactions in the Coronavirus Genome Form High-Order Structures Promoting Discontinuous RNA Synthesis during Transcription

Journal: Journal of Virology

doi: 10.1128/JVI.01782-12

Relevance of active domain regions. (Left) Mfold secondary structure prediction of the active domain. Regions A, B, and C are indicated by circles. (Right) qRT-PCR analysis of N sgmRNA levels normalized to gRNA (N sgmRNA/gRNA) and referred to the level
Figure Legend Snippet: Relevance of active domain regions. (Left) Mfold secondary structure prediction of the active domain. Regions A, B, and C are indicated by circles. (Right) qRT-PCR analysis of N sgmRNA levels normalized to gRNA (N sgmRNA/gRNA) and referred to the level

Techniques Used: Quantitative RT-PCR

Related Articles

Diagnostic Assay:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany). .. The reaction mixture (15 µL) included template cDNA (0.5 µg), 0.75 µM of each primer, and 1X SYBR-Green mix (Fast Start DNA Master plus, Roche Diagnostic Co.).

Amplification:

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: The cDNA fragments of nine Tolls were amplified using the gene specific primers ( ) under the following conditions: 1 cycle of 94°C for 2 min, 28 cycles of 94°C for 30 s, 60°C for 30 s, 72°C for 30 s, followed by elongation at 72°C for 5 min. As an internal loading control, the shrimp EF1α ( ) was amplified as the same PCR conditions. .. The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ).

Synthesized:

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells
Article Snippet: .. Complementary DNA was synthesized using a Revertra Ace qPCR Kit (Toyobo; FSQ-101) and subjected to qRT-PCR analysis with Faststart SYBR master mix (4673484, Roche) and a Thermal Cycler Dice Real Time system (Takara). .. RNA-sequencing analysis RNA-sequence libraries were prepared with NeoPrep (Illumina) using TruSeq Stranded mRNA NeoPrep Kit (Illumina).

Quantitative RT-PCR:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: .. The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany). .. The qRT-PCR assays were performed using the Light Cycler system (Roche Diagnostics GmbH).

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: .. Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems). .. Primers for mRNA expression are shown in online.

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Article Snippet: .. For qRT-PCR analysis we used Roche’s Lightcycler and Stratagene’s RT kit. .. RNA-seq library preparation (related to , ) We followed protocols previously described (Wapinski et al., 2013).

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Article Title: Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing
Article Snippet: .. To validate the RNA-Seq results, 9 DEGs were subjected to qRT-PCR analysis performed on a LightCycler480 real-time PCR system (Roche, Basel, Switzerland). .. Relative gene expression levels were evaluated according to a previous method [ ].

Article Title: Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells
Article Snippet: .. Quantitative real-time PCR (qRT-PCR) PCOS-specific DEGs between MGCs and CCs were validated with quantitative real-time PCR (qRT-PCR). qRT-PCR analysis was performed on the Roche LightCycler® 480 using gene-specific primers and SYBR Green I Master mix (Roche). ..

Article Title: Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane
Article Snippet: .. qRT-PCR analysis To analyze the expression patterns of the ScJAZ family genes in different sugarcane tissues and in response to various adverse stressors, qRT-PCR was conducted using SYBR Green Master (ROX) (Roche, China) and an ABI 7500 qRT-PCR system (Applied Biosystems, South San Francisco, CA, USA). ..

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: .. The qRT-PCR analysis was performed using Fast start essential DNA green master mix (Roche) as per the manufacturer’s instructions. .. DDX39B levels were perturbed in HEK293 cells by transfecting with control siRNA or siDDX39B-1 or pEGFP-C1 vector or pEGFP-DDX39B construct.

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: .. Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche). ..

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: .. M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche). .. Unpaired two-tailed Student’s t-test was used for statistical analysis.

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: .. After 48 hours of transfection, total RNA was isolated and reverse transcribed using random hexamers. qRT-PCR analysis of DDX39B or DDX49 transcripts was performed using Fast start essential DNA green master mix (Roche). ..

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells
Article Snippet: .. Complementary DNA was synthesized using a Revertra Ace qPCR Kit (Toyobo; FSQ-101) and subjected to qRT-PCR analysis with Faststart SYBR master mix (4673484, Roche) and a Thermal Cycler Dice Real Time system (Takara). .. RNA-sequencing analysis RNA-sequence libraries were prepared with NeoPrep (Illumina) using TruSeq Stranded mRNA NeoPrep Kit (Illumina).

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: .. The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ). ..

Article Title: Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis
Article Snippet: .. DNA-free RNA samples from lung tissue of five vaccinated mice were extracted with TRIzol reagent (Invitrogen), respectively. qRT-PCR analysis was performed using SYBR Green kit (Roche) and Applied Rotor-Gene 3000 Real-Time system (Gene) with different specific primers listed in , including IFN-γ, IL-10, TNF-α, and iNOS. ..

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway
Article Snippet: .. Real-time quantitative RT-PCR Cells were kept in DMEM/F12 with 0.1% FBS for 12 h before each experiment, and then NT-4 was applied at the indicated concentrations in fresh DMEM/F12 medium containing 0.1% FBS for 12 h. Total mRNA was extracted from cultured Schwann cells by using Trizol, and cDNA was produced using the GoScript™ Reverse Transcription System. qRT-PCR analysis was performed on a Roche LightCycler 480 for real-time PCR, using GoTaq® qPCR Master Mix with the following primers: truncated TrkB, F: 5′-AATGGAGACTACACCCTAATGGC-3′, R: 5′-GCAGGCAGAATCCTACCACAG-3′; p75NTR, F: 5′-ACATTCTCCGATGTGGTGAGC-3′, R: 5′-CCTCGTCCTGGTAGTAGCCATA-3′; MBP, F: 5′-AGAGTCCGACGAGCTTCAGA-3′, R: 5′-CAGGTACTTGGATCGCTGTG-3′; MPZ, F: 5′-TCTCAGGTCACGCTCTATGTC-3′, R: 5′-GCCAGCAGTACCGAATCAG-3′; PMP22, F: 5′-CCCAACTCCCAGCCACCATG-3′, R: 5′-TCATTCGCGTTTCCGCAGGATC-3′; and GAPDH, F: 5′-GTATGTCGTGGAGTCTACTGGCGT-3′, R: 5′-TACTCCTTGGAGGCCATGTAGGCC-3′. ..

SYBR Green Assay:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany). .. The reaction mixture (15 µL) included template cDNA (0.5 µg), 0.75 µM of each primer, and 1X SYBR-Green mix (Fast Start DNA Master plus, Roche Diagnostic Co.).

Article Title: Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells
Article Snippet: .. Quantitative real-time PCR (qRT-PCR) PCOS-specific DEGs between MGCs and CCs were validated with quantitative real-time PCR (qRT-PCR). qRT-PCR analysis was performed on the Roche LightCycler® 480 using gene-specific primers and SYBR Green I Master mix (Roche). ..

Article Title: Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane
Article Snippet: .. qRT-PCR analysis To analyze the expression patterns of the ScJAZ family genes in different sugarcane tissues and in response to various adverse stressors, qRT-PCR was conducted using SYBR Green Master (ROX) (Roche, China) and an ABI 7500 qRT-PCR system (Applied Biosystems, South San Francisco, CA, USA). ..

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: .. Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche). ..

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: .. M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche). .. Unpaired two-tailed Student’s t-test was used for statistical analysis.

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: .. The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ). ..

Article Title: Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis
Article Snippet: .. DNA-free RNA samples from lung tissue of five vaccinated mice were extracted with TRIzol reagent (Invitrogen), respectively. qRT-PCR analysis was performed using SYBR Green kit (Roche) and Applied Rotor-Gene 3000 Real-Time system (Gene) with different specific primers listed in , including IFN-γ, IL-10, TNF-α, and iNOS. ..

Two Tailed Test:

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche). .. Unpaired two-tailed Student’s t-test was used for statistical analysis.

Expressing:

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems). .. Primers for mRNA expression are shown in online.

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Article Title: Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing
Article Snippet: To validate the RNA-Seq results, 9 DEGs were subjected to qRT-PCR analysis performed on a LightCycler480 real-time PCR system (Roche, Basel, Switzerland). .. Relative gene expression levels were evaluated according to a previous method [ ].

Article Title: Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane
Article Snippet: .. qRT-PCR analysis To analyze the expression patterns of the ScJAZ family genes in different sugarcane tissues and in response to various adverse stressors, qRT-PCR was conducted using SYBR Green Master (ROX) (Roche, China) and an ABI 7500 qRT-PCR system (Applied Biosystems, South San Francisco, CA, USA). ..

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: For analysis of Plxnb2 expression in niche cells and central BM, whole BM cells were isolated from femur and tibiae by flushing, and total RNA was extracted by Trizol. .. M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche).

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: After 48 hours of transfection, total RNA was isolated and reverse transcribed using random hexamers. qRT-PCR analysis of DDX39B or DDX49 transcripts was performed using Fast start essential DNA green master mix (Roche). .. DDX39B and DDX49 expression was normalized to the expression of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and presented relative to the control siRNA sample ( and Figure S2).

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ). .. Expression level of each gene was calculated relative to internal control gene EF-1α by using the Livak (2-ΔΔCT ) method.

Article Title: Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis
Article Snippet: Paragraph title: Cytokines and iNOS mRNA expression in the lung detected by qRT-PCR ... DNA-free RNA samples from lung tissue of five vaccinated mice were extracted with TRIzol reagent (Invitrogen), respectively. qRT-PCR analysis was performed using SYBR Green kit (Roche) and Applied Rotor-Gene 3000 Real-Time system (Gene) with different specific primers listed in , including IFN-γ, IL-10, TNF-α, and iNOS.

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway
Article Snippet: Real-time quantitative RT-PCR Cells were kept in DMEM/F12 with 0.1% FBS for 12 h before each experiment, and then NT-4 was applied at the indicated concentrations in fresh DMEM/F12 medium containing 0.1% FBS for 12 h. Total mRNA was extracted from cultured Schwann cells by using Trizol, and cDNA was produced using the GoScript™ Reverse Transcription System. qRT-PCR analysis was performed on a Roche LightCycler 480 for real-time PCR, using GoTaq® qPCR Master Mix with the following primers: truncated TrkB, F: 5′-AATGGAGACTACACCCTAATGGC-3′, R: 5′-GCAGGCAGAATCCTACCACAG-3′; p75NTR, F: 5′-ACATTCTCCGATGTGGTGAGC-3′, R: 5′-CCTCGTCCTGGTAGTAGCCATA-3′; MBP, F: 5′-AGAGTCCGACGAGCTTCAGA-3′, R: 5′-CAGGTACTTGGATCGCTGTG-3′; MPZ, F: 5′-TCTCAGGTCACGCTCTATGTC-3′, R: 5′-GCCAGCAGTACCGAATCAG-3′; PMP22, F: 5′-CCCAACTCCCAGCCACCATG-3′, R: 5′-TCATTCGCGTTTCCGCAGGATC-3′; and GAPDH, F: 5′-GTATGTCGTGGAGTCTACTGGCGT-3′, R: 5′-TACTCCTTGGAGGCCATGTAGGCC-3′. .. Relative expression values for each mRNA were obtained by normalizing them to GAPDH expression, and differences between samples were calculated using the 2(−ΔΔC(T)) method (Livak & Schmittgen ).

Hybridization:

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: Total RNA was extracted from Southern hybridization positive (T1 ) and NT plants using a RNAqueous kit (Ambion Inc., Austin, USA) and the DNA contamination were eliminated by treatment with DNase I. RT-PCR was performed by a one-step RT-PCR kit (Qiagen, USA) as instructed by the manufacturer. .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany).

Transfection:

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: Cells were transfected with stealth RNA duplexes using Lipofectamine RNAiMAX (Invitrogen). .. Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems).

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: .. After 48 hours of transfection, total RNA was isolated and reverse transcribed using random hexamers. qRT-PCR analysis of DDX39B or DDX49 transcripts was performed using Fast start essential DNA green master mix (Roche). ..

Sequencing:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: Quantitative real-time polymerase chain reaction (qRT-PCR) The levels of HPN 1 and HPN 3 transcripts were assessed using a primer set specific for a conserved sequence of these peptides ( ). shows the primer sequences applied in qRT-PCR for HPN 1-3 and LL-37. .. The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany).

Cell Culture:

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway
Article Snippet: .. Real-time quantitative RT-PCR Cells were kept in DMEM/F12 with 0.1% FBS for 12 h before each experiment, and then NT-4 was applied at the indicated concentrations in fresh DMEM/F12 medium containing 0.1% FBS for 12 h. Total mRNA was extracted from cultured Schwann cells by using Trizol, and cDNA was produced using the GoScript™ Reverse Transcription System. qRT-PCR analysis was performed on a Roche LightCycler 480 for real-time PCR, using GoTaq® qPCR Master Mix with the following primers: truncated TrkB, F: 5′-AATGGAGACTACACCCTAATGGC-3′, R: 5′-GCAGGCAGAATCCTACCACAG-3′; p75NTR, F: 5′-ACATTCTCCGATGTGGTGAGC-3′, R: 5′-CCTCGTCCTGGTAGTAGCCATA-3′; MBP, F: 5′-AGAGTCCGACGAGCTTCAGA-3′, R: 5′-CAGGTACTTGGATCGCTGTG-3′; MPZ, F: 5′-TCTCAGGTCACGCTCTATGTC-3′, R: 5′-GCCAGCAGTACCGAATCAG-3′; PMP22, F: 5′-CCCAACTCCCAGCCACCATG-3′, R: 5′-TCATTCGCGTTTCCGCAGGATC-3′; and GAPDH, F: 5′-GTATGTCGTGGAGTCTACTGGCGT-3′, R: 5′-TACTCCTTGGAGGCCATGTAGGCC-3′. ..

Reverse Transcription Polymerase Chain Reaction:

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: Paragraph title: Reverse transcriptase-PCR (RT-PCR) and Quantitative real-time PCR (qRT-PCR) ... The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany).

Nucleic Acid Electrophoresis:

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: RNA quantity and quality was determined using both Nanodrop2000-C spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and gel electrophoresis. .. Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche).

In Vivo:

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: Quantitative reverse transcription PCR (qRT-PCR) was conducted to detect the mRNA levels of genes (Tolls, Toll pathway components or AMPs) under the pathogenic challenge experiments or RNAi in vivo . .. The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ).

RNA Sequencing Assay:

Article Title: Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing
Article Snippet: .. To validate the RNA-Seq results, 9 DEGs were subjected to qRT-PCR analysis performed on a LightCycler480 real-time PCR system (Roche, Basel, Switzerland). .. Relative gene expression levels were evaluated according to a previous method [ ].

Isolation:

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: .. Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems). .. Primers for mRNA expression are shown in online.

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Article Snippet: Isolated RNA was subjected to DNAse treatment using TurboDNase and purified by phenol-chloroform extraction and ethanol precipitation. .. For qRT-PCR analysis we used Roche’s Lightcycler and Stratagene’s RT kit.

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: Total RNA was isolated using RNAprep Pure Plant kit (TIANGEN, Beijing, China). .. Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche).

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: For analysis of Plxnb2 expression in niche cells and central BM, whole BM cells were isolated from femur and tibiae by flushing, and total RNA was extracted by Trizol. .. M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche).

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: .. After 48 hours of transfection, total RNA was isolated and reverse transcribed using random hexamers. qRT-PCR analysis of DDX39B or DDX49 transcripts was performed using Fast start essential DNA green master mix (Roche). ..

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells
Article Snippet: RT-qPCR analysis Total RNA was isolated from FACS-sorted Treg cells using an RNeasy Plus Mini Kit (Qiagen; 74136). .. Complementary DNA was synthesized using a Revertra Ace qPCR Kit (Toyobo; FSQ-101) and subjected to qRT-PCR analysis with Faststart SYBR master mix (4673484, Roche) and a Thermal Cycler Dice Real Time system (Takara).

Negative Control:

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: Validated Stealth negative control RNAi duplex with high GC content (Invitrogen) was used as a control. qRT–PCR analysis. .. Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems).

Purification:

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Article Snippet: Isolated RNA was subjected to DNAse treatment using TurboDNase and purified by phenol-chloroform extraction and ethanol precipitation. .. For qRT-PCR analysis we used Roche’s Lightcycler and Stratagene’s RT kit.

Polymerase Chain Reaction:

Article Title: A member of the ETS family, EHF, and the ATPase RUVBL1 inhibit p53-mediated apoptosis
Article Snippet: .. Total RNA was isolated using the TRIsure (BIOLINE), and 1 mg RNA was reverse transcribed with SuperScript III Reverse transcriptase (Invitrogen) using an oligo(dT)18 primer. qRT–PCR analysis of cDNA and genomic DNA was performed on a LightCycler 480 (Roche Applied Science) with Syber Green PCR mastermix (Applied Biosystems). .. Primers for mRNA expression are shown in online.

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: The PCR amplification profile consisted of an initial denaturation of cDNA at 95 °C for 5 min and followed by 28 cycles for 40 s at 94 °C, 40 s at 58 °C and 20 s at 72 °C, followed by a final extension at 72 °C for 5 min. .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany).

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: .. M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche). .. Unpaired two-tailed Student’s t-test was used for statistical analysis.

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: Paragraph title: Semi-quantitative and quantitative reverse transcription PCR ... The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ).

Staining:

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Mouse Assay:

Article Title: Comparison of BCG prime-DNA booster and rBCG regimens for protection against tuberculosis
Article Snippet: .. DNA-free RNA samples from lung tissue of five vaccinated mice were extracted with TRIzol reagent (Invitrogen), respectively. qRT-PCR analysis was performed using SYBR Green kit (Roche) and Applied Rotor-Gene 3000 Real-Time system (Gene) with different specific primers listed in , including IFN-γ, IL-10, TNF-α, and iNOS. ..

Chromatin Immunoprecipitation:

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: Paragraph title: Chromatin immunoprecipitation ... The qRT-PCR analysis was performed using Fast start essential DNA green master mix (Roche) as per the manufacturer’s instructions.

Software:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: .. The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany). .. The qRT-PCR assays were performed using the Light Cycler system (Roche Diagnostics GmbH).

Article Title: Plant jasmonate ZIM domain genes: shedding light on structure and expression patterns of JAZ gene family in sugarcane
Article Snippet: qRT-PCR analysis To analyze the expression patterns of the ScJAZ family genes in different sugarcane tissues and in response to various adverse stressors, qRT-PCR was conducted using SYBR Green Master (ROX) (Roche, China) and an ABI 7500 qRT-PCR system (Applied Biosystems, South San Francisco, CA, USA). .. Beacon Designer 8.12 software was used to design the specific qRT-PCR primers (Table ) based on the unigene sequences of ScJAZ1 –ScJAZ7 .

Real-time Polymerase Chain Reaction:

Article Title: Antimicrobial peptides and nitric oxide production by neutrophils from periodontitis subjects
Article Snippet: Paragraph title: Quantitative real-time polymerase chain reaction (qRT-PCR) ... The sequences of the primers for qRT-PCR analysis were obtained using the Light-Cycler software (Roche Diagnostics GmbH, Germany).

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Article Title: Exploration of the Effect of Blue Light on Functional Metabolite Accumulation in Longan Embryonic Calli via RNA Sequencing
Article Snippet: .. To validate the RNA-Seq results, 9 DEGs were subjected to qRT-PCR analysis performed on a LightCycler480 real-time PCR system (Roche, Basel, Switzerland). .. Relative gene expression levels were evaluated according to a previous method [ ].

Article Title: Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells
Article Snippet: .. Quantitative real-time PCR (qRT-PCR) PCOS-specific DEGs between MGCs and CCs were validated with quantitative real-time PCR (qRT-PCR). qRT-PCR analysis was performed on the Roche LightCycler® 480 using gene-specific primers and SYBR Green I Master mix (Roche). ..

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: Paragraph title: Quantitative real time PCR and immunoblotting to investigate the knock-down efficiency ... After 48 hours of transfection, total RNA was isolated and reverse transcribed using random hexamers. qRT-PCR analysis of DDX39B or DDX49 transcripts was performed using Fast start essential DNA green master mix (Roche).

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells
Article Snippet: .. Complementary DNA was synthesized using a Revertra Ace qPCR Kit (Toyobo; FSQ-101) and subjected to qRT-PCR analysis with Faststart SYBR master mix (4673484, Roche) and a Thermal Cycler Dice Real Time system (Takara). .. RNA-sequencing analysis RNA-sequence libraries were prepared with NeoPrep (Illumina) using TruSeq Stranded mRNA NeoPrep Kit (Illumina).

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway
Article Snippet: .. Real-time quantitative RT-PCR Cells were kept in DMEM/F12 with 0.1% FBS for 12 h before each experiment, and then NT-4 was applied at the indicated concentrations in fresh DMEM/F12 medium containing 0.1% FBS for 12 h. Total mRNA was extracted from cultured Schwann cells by using Trizol, and cDNA was produced using the GoScript™ Reverse Transcription System. qRT-PCR analysis was performed on a Roche LightCycler 480 for real-time PCR, using GoTaq® qPCR Master Mix with the following primers: truncated TrkB, F: 5′-AATGGAGACTACACCCTAATGGC-3′, R: 5′-GCAGGCAGAATCCTACCACAG-3′; p75NTR, F: 5′-ACATTCTCCGATGTGGTGAGC-3′, R: 5′-CCTCGTCCTGGTAGTAGCCATA-3′; MBP, F: 5′-AGAGTCCGACGAGCTTCAGA-3′, R: 5′-CAGGTACTTGGATCGCTGTG-3′; MPZ, F: 5′-TCTCAGGTCACGCTCTATGTC-3′, R: 5′-GCCAGCAGTACCGAATCAG-3′; PMP22, F: 5′-CCCAACTCCCAGCCACCATG-3′, R: 5′-TCATTCGCGTTTCCGCAGGATC-3′; and GAPDH, F: 5′-GTATGTCGTGGAGTCTACTGGCGT-3′, R: 5′-TACTCCTTGGAGGCCATGTAGGCC-3′. ..

RNA Extraction:

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Article Snippet: Proteinase K treatment proceeded for 45 min at 45C, followed by RNA extraction using Trizol. .. For qRT-PCR analysis we used Roche’s Lightcycler and Stratagene’s RT kit.

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: Paragraph title: RNA extraction, cDNA synthesis, and qRT-PCR analysis ... Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche).

Article Title: RNAi screening identifies a new Toll from shrimp Litopenaeus vannamei that restricts WSSV infection through activating Dorsal to induce antimicrobial peptides
Article Snippet: .. The method of tissues collection, total RNA extraction and cDNA synthesis was as described above. qRT-PCR analysis was performed in the LightCycler 480 System (Roche, Germany) with a volume of 10 μl comprised of 1 μl of 1:10 cDNA diluted with ddH2 O, 5 μl of 2 × SYBR Green Master Mix (Takara, Japan), and 250 nM of each primer ( ). ..

Agarose Gel Electrophoresis:

Article Title: Pea p68, a DEAD-box helicase, enhances salt tolerance in marker-free transgenic plants of soybean [Glycine max (L.) Merrill]
Article Snippet: .. The amplified products were determined on a 1.0% agarose gel (Sigma, St. Louis, USA) stained with 0.1% ethidium bromide (Sigma, St. Louis, USA) and photographed using the Gel Documentation system (UVITEC, Cambridge, UK). qRT-PCR analysis was performed in LightCycler® 480 Real-time PCR system (Roche, Germany). .. The expression analysis of the RT-PCR positive (T1 ) and NT plants were conducted using Prime Script™ RT Reagent Kit (Takara Bio Inc, Japan) and p68 gene-specific primer set (FP: 5′-CCTCGCATTCTCTTCCTCGTA-3′ and RP: 5′-CGACGAGAACCATTGGCTAGA-3′) (Banu et al. ).

Ethanol Precipitation:

Article Title: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders
Article Snippet: Isolated RNA was subjected to DNAse treatment using TurboDNase and purified by phenol-chloroform extraction and ethanol precipitation. .. For qRT-PCR analysis we used Roche’s Lightcycler and Stratagene’s RT kit.

Spectrophotometry:

Article Title: Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture
Article Snippet: RNA quantity and quality was determined using both Nanodrop2000-C spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and gel electrophoresis. .. Detailed information of all the primers used in this study is listed in Additional file : Table S4. qRT-PCR analysis was performed on a LightCycler TM 480 II System (Roche Applied Science, Basel, Switzerland) using LightCycler 480 SYBR green 1 Master mix (Roche).

Produced:

Article Title: Neurotrophin-4 induces myelin protein zero expression in cultured Schwann cells via the TrkB/PI3K/Akt/mTORC1 pathway
Article Snippet: .. Real-time quantitative RT-PCR Cells were kept in DMEM/F12 with 0.1% FBS for 12 h before each experiment, and then NT-4 was applied at the indicated concentrations in fresh DMEM/F12 medium containing 0.1% FBS for 12 h. Total mRNA was extracted from cultured Schwann cells by using Trizol, and cDNA was produced using the GoScript™ Reverse Transcription System. qRT-PCR analysis was performed on a Roche LightCycler 480 for real-time PCR, using GoTaq® qPCR Master Mix with the following primers: truncated TrkB, F: 5′-AATGGAGACTACACCCTAATGGC-3′, R: 5′-GCAGGCAGAATCCTACCACAG-3′; p75NTR, F: 5′-ACATTCTCCGATGTGGTGAGC-3′, R: 5′-CCTCGTCCTGGTAGTAGCCATA-3′; MBP, F: 5′-AGAGTCCGACGAGCTTCAGA-3′, R: 5′-CAGGTACTTGGATCGCTGTG-3′; MPZ, F: 5′-TCTCAGGTCACGCTCTATGTC-3′, R: 5′-GCCAGCAGTACCGAATCAG-3′; PMP22, F: 5′-CCCAACTCCCAGCCACCATG-3′, R: 5′-TCATTCGCGTTTCCGCAGGATC-3′; and GAPDH, F: 5′-GTATGTCGTGGAGTCTACTGGCGT-3′, R: 5′-TACTCCTTGGAGGCCATGTAGGCC-3′. ..

Immunoprecipitation:

Article Title: DDX39B promotes translation through regulation of pre-ribosomal RNA levels
Article Snippet: For immunoprecipitation, 15 µg of rabbit IgG (CST, #2729) or DDX39B antibody (Abcam, ab181061) and 15 µg of chromatin was used. .. The qRT-PCR analysis was performed using Fast start essential DNA green master mix (Roche) as per the manufacturer’s instructions.

FACS:

Article Title: JunB regulates homeostasis and suppressive functions of effector regulatory T cells
Article Snippet: RT-qPCR analysis Total RNA was isolated from FACS-sorted Treg cells using an RNeasy Plus Mini Kit (Qiagen; 74136). .. Complementary DNA was synthesized using a Revertra Ace qPCR Kit (Toyobo; FSQ-101) and subjected to qRT-PCR analysis with Faststart SYBR master mix (4673484, Roche) and a Thermal Cycler Dice Real Time system (Takara).

T-Test:

Article Title: Plexin-B2 mediates physiologic and pathologic functions of angiogenin
Article Snippet: M-MLV reverse transcriptase (Promega) was used to reverse transcribe total RNA into cDNA, per manufacturer’s instructions. qRT-PCR analysis was performed on a LightCycler 480 II (Roche) using SYBR Green PCR mix (Roche). .. Unpaired two-tailed Student’s t-test was used for statistical analysis.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 88
    Roche qrt pcr analysis total rna
    Quercetin increases uncoupling protein-1 ( Ucp1) gene expression specifically in subcutaneous white adipose tissue. Gene expression in sWAT ( A ) and BAT ( B ) was determined by <t>qRT-PCR.</t> Hematoxylin and eosin (H E) staining was performed on paraffin-embedded sWAT sections, and representative pictures are shown ( C ). Pictures were analyzed in ImageJ to determine the relative cell size ( D ). sWAT sections were stained for UCP-1 (arrows indicate UCP-1 positive cells, E ) as well. BAT sections were stained for H E ( F ) and used to quantify lipid droplet content in ImageJ ( G ). BAT sections were also stained for UCP-1 ( H ). Data are represented as mean ± SEM ( n = 8–10); the expression of genes was corrected for the reference gene β 2-microglobulin (sWAT), Gapdh , and Hprt (BAT), * p
    Qrt Pcr Analysis Total Rna, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qrt pcr analysis total rna/product/Roche
    Average 88 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    qrt pcr analysis total rna - by Bioz Stars, 2020-02
    88/100 stars
      Buy from Supplier

    78
    Roche quantitative real time pcr qrt pcr analysis qrt pcr analyses
    Features of miR-17-5p and ETV1 expression in TNBC cells and clinical samples. a , b , <t>QRT-PCR</t> analyses of miR-17-5p and ETV1 expression levels in TNBC cells. c , d , The expression levels of miR-17-5p and ETV1 in clinical TNBC samples evaluated by qRT-PCR. Data are expressed as the mean ± SEM of three independent experiments. ** P
    Quantitative Real Time Pcr Qrt Pcr Analysis Qrt Pcr Analyses, supplied by Roche, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/quantitative real time pcr qrt pcr analysis qrt pcr analyses/product/Roche
    Average 78 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    quantitative real time pcr qrt pcr analysis qrt pcr analyses - by Bioz Stars, 2020-02
    78/100 stars
      Buy from Supplier

    78
    Roche rt pcr qrt pcr cdna
    Sfl1-mediated repression is important for FLO11 regulation but is absent in the 133d strain. (A) Northern blot analysis of FLO11 mRNA, as described in , for the indicated wild-type and mutant strains. (B) <t>qRT-PCR</t> analysis of FLO11 and SFL1 expression
    Rt Pcr Qrt Pcr Cdna, supplied by Roche, used in various techniques. Bioz Stars score: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rt pcr qrt pcr cdna/product/Roche
    Average 78 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rt pcr qrt pcr cdna - by Bioz Stars, 2020-02
    78/100 stars
      Buy from Supplier

    81
    Roche qrt pcr analysis qrt pcr
    Verification of RNA-seq results by <t>qRT-PCR.</t> The DEGs in GXU-34176 vs GXU-34140 related to the category of ‘abscisic acid-activated signaling pathway’ (c71654.graph_c0 and c65832.graph_c0), ‘leaf senescence’ (c64240.graph_c0), ‘response to ethylene’ (c67492.graph_c0) and ‘cell wall modification involved in abscission’ (c65986.graph_c0). The DEGs in GN18 vs FN95–1702 related to the category of ‘response to water deprivation’ (c54647.graph_c0, c56804.graph_c0 and c61335.graph_c0) and ‘response to oxidative stress’ (c57471.graph_c0). The DEGs in GUC2 vs GUC10 related to the category of ‘ubiquitin-protein transferase activity’ (c69746.graph_c0), ‘defense response to fungus’ (c72075.graph_c0), ‘response to jasmonic acid’ (c65355.graph_c0). Data of qRT-PCR are presented as mean ± SD (n = 9) and error bars represent SD.
    Qrt Pcr Analysis Qrt Pcr, supplied by Roche, used in various techniques. Bioz Stars score: 81/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qrt pcr analysis qrt pcr/product/Roche
    Average 81 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    qrt pcr analysis qrt pcr - by Bioz Stars, 2020-02
    81/100 stars
      Buy from Supplier

    Image Search Results


    Quercetin increases uncoupling protein-1 ( Ucp1) gene expression specifically in subcutaneous white adipose tissue. Gene expression in sWAT ( A ) and BAT ( B ) was determined by qRT-PCR. Hematoxylin and eosin (H E) staining was performed on paraffin-embedded sWAT sections, and representative pictures are shown ( C ). Pictures were analyzed in ImageJ to determine the relative cell size ( D ). sWAT sections were stained for UCP-1 (arrows indicate UCP-1 positive cells, E ) as well. BAT sections were stained for H E ( F ) and used to quantify lipid droplet content in ImageJ ( G ). BAT sections were also stained for UCP-1 ( H ). Data are represented as mean ± SEM ( n = 8–10); the expression of genes was corrected for the reference gene β 2-microglobulin (sWAT), Gapdh , and Hprt (BAT), * p

    Journal: International Journal of Molecular Sciences

    Article Title: Quercetin Lowers Plasma Triglycerides Accompanied by White Adipose Tissue Browning in Diet-Induced Obese Mice

    doi: 10.3390/ijms19061786

    Figure Lengend Snippet: Quercetin increases uncoupling protein-1 ( Ucp1) gene expression specifically in subcutaneous white adipose tissue. Gene expression in sWAT ( A ) and BAT ( B ) was determined by qRT-PCR. Hematoxylin and eosin (H E) staining was performed on paraffin-embedded sWAT sections, and representative pictures are shown ( C ). Pictures were analyzed in ImageJ to determine the relative cell size ( D ). sWAT sections were stained for UCP-1 (arrows indicate UCP-1 positive cells, E ) as well. BAT sections were stained for H E ( F ) and used to quantify lipid droplet content in ImageJ ( G ). BAT sections were also stained for UCP-1 ( H ). Data are represented as mean ± SEM ( n = 8–10); the expression of genes was corrected for the reference gene β 2-microglobulin (sWAT), Gapdh , and Hprt (BAT), * p

    Article Snippet: RNA Isolation and qRT-PCR Analysis Total RNA was isolated using TriPure Isolation reagent (Roche obtained via Sigma, St. Louis, MO, USA ) following the manufacturer’s protocol. cDNA was made using Moloney Murine Leukemia Virus Reverse Transcriptase (Promega, Leiden, The Netherlands).

    Techniques: Expressing, Quantitative RT-PCR, Staining

    Quercetin reduces hepatic apolipoprotein B ( Apob) expression and increases the uptake of triglycerides (TG)-derived fatty acid (FA) by subcutaneous white adipose tissue. In week 2 and week 10 of the intervention, 24 h feces was collected ( A ) and used to determine fecal free fatty acid (FFA) concentration ( B ). Gene expression in the liver was determined by qRT-PCR for acyl-CoA synthetase long-chain family member 1 ( Acsl1) , acetyl-CoA carboxylase 2 ( Acc2 ), microsomal triglyceride transfer protein ( Mttp ), and Apob ( C ). After 12 weeks, mice were injected with glycerol tri[ 3 H]oleate-labeled lipoprotein-like particles, and clearance from plasma ( D ) and uptake per gram organ ( E ) were determined by 3 H-activity analysis. Data are represented as mean ± SEM ( n = 8–10); the expression of genes was corrected for the reference gene β2-microglobulin , * p

    Journal: International Journal of Molecular Sciences

    Article Title: Quercetin Lowers Plasma Triglycerides Accompanied by White Adipose Tissue Browning in Diet-Induced Obese Mice

    doi: 10.3390/ijms19061786

    Figure Lengend Snippet: Quercetin reduces hepatic apolipoprotein B ( Apob) expression and increases the uptake of triglycerides (TG)-derived fatty acid (FA) by subcutaneous white adipose tissue. In week 2 and week 10 of the intervention, 24 h feces was collected ( A ) and used to determine fecal free fatty acid (FFA) concentration ( B ). Gene expression in the liver was determined by qRT-PCR for acyl-CoA synthetase long-chain family member 1 ( Acsl1) , acetyl-CoA carboxylase 2 ( Acc2 ), microsomal triglyceride transfer protein ( Mttp ), and Apob ( C ). After 12 weeks, mice were injected with glycerol tri[ 3 H]oleate-labeled lipoprotein-like particles, and clearance from plasma ( D ) and uptake per gram organ ( E ) were determined by 3 H-activity analysis. Data are represented as mean ± SEM ( n = 8–10); the expression of genes was corrected for the reference gene β2-microglobulin , * p

    Article Snippet: RNA Isolation and qRT-PCR Analysis Total RNA was isolated using TriPure Isolation reagent (Roche obtained via Sigma, St. Louis, MO, USA ) following the manufacturer’s protocol. cDNA was made using Moloney Murine Leukemia Virus Reverse Transcriptase (Promega, Leiden, The Netherlands).

    Techniques: Expressing, Derivative Assay, Concentration Assay, Quantitative RT-PCR, Mouse Assay, Injection, Labeling, Activity Assay

    Features of miR-17-5p and ETV1 expression in TNBC cells and clinical samples. a , b , QRT-PCR analyses of miR-17-5p and ETV1 expression levels in TNBC cells. c , d , The expression levels of miR-17-5p and ETV1 in clinical TNBC samples evaluated by qRT-PCR. Data are expressed as the mean ± SEM of three independent experiments. ** P

    Journal: BMC Cancer

    Article Title: miR-17-5p suppresses cell proliferation and invasion by targeting ETV1 in triple-negative breast cancer

    doi: 10.1186/s12885-017-3674-x

    Figure Lengend Snippet: Features of miR-17-5p and ETV1 expression in TNBC cells and clinical samples. a , b , QRT-PCR analyses of miR-17-5p and ETV1 expression levels in TNBC cells. c , d , The expression levels of miR-17-5p and ETV1 in clinical TNBC samples evaluated by qRT-PCR. Data are expressed as the mean ± SEM of three independent experiments. ** P

    Article Snippet: Quantitative real time PCR (qRT-PCR) analysis qRT-PCR analyses of miR-17-5p and ETV1 expression were performed on a LightCycler 480 (Roche Diagnostics, Germany) according to our previous report [ ].

    Techniques: Expressing, Quantitative RT-PCR

    ETV1 is a direct target of miR-17-5p in TNBC cells. a , Target sequences of miR-17-5p in ETV1 3′-UTR and mutant sites in 3′-UTR. b , Relative luciferase activity of ETV1 3′-UTR and mutant in the miR-17-5p mimic-transfected 293 T cells. c , d , The effect of miR-17-5p on ETV1 expression in MDA-MB-231 and BT549 cells was detected by qRT-PCR and western blotting after the cells were transfected with miR-17-5p mimic or inhibitor, respectively. e , The effect of miR-17-5p on ETV1 expression was also observed in MCF10A cells by co-transfecting with GV141-ETV1 and miR-17-5p inhibitor. Data are expressed as the mean ± SEM of three independent experiments. * P

    Journal: BMC Cancer

    Article Title: miR-17-5p suppresses cell proliferation and invasion by targeting ETV1 in triple-negative breast cancer

    doi: 10.1186/s12885-017-3674-x

    Figure Lengend Snippet: ETV1 is a direct target of miR-17-5p in TNBC cells. a , Target sequences of miR-17-5p in ETV1 3′-UTR and mutant sites in 3′-UTR. b , Relative luciferase activity of ETV1 3′-UTR and mutant in the miR-17-5p mimic-transfected 293 T cells. c , d , The effect of miR-17-5p on ETV1 expression in MDA-MB-231 and BT549 cells was detected by qRT-PCR and western blotting after the cells were transfected with miR-17-5p mimic or inhibitor, respectively. e , The effect of miR-17-5p on ETV1 expression was also observed in MCF10A cells by co-transfecting with GV141-ETV1 and miR-17-5p inhibitor. Data are expressed as the mean ± SEM of three independent experiments. * P

    Article Snippet: Quantitative real time PCR (qRT-PCR) analysis qRT-PCR analyses of miR-17-5p and ETV1 expression were performed on a LightCycler 480 (Roche Diagnostics, Germany) according to our previous report [ ].

    Techniques: Mutagenesis, Luciferase, Activity Assay, Transfection, Expressing, Multiple Displacement Amplification, Quantitative RT-PCR, Western Blot

    Sfl1-mediated repression is important for FLO11 regulation but is absent in the 133d strain. (A) Northern blot analysis of FLO11 mRNA, as described in , for the indicated wild-type and mutant strains. (B) qRT-PCR analysis of FLO11 and SFL1 expression

    Journal: Genetics

    Article Title: Chromatin Modulation at the FLO11 Promoter of Saccharomyces cerevisiae by HDAC and Swi/Snf Complexes

    doi: 10.1534/genetics.112.140301

    Figure Lengend Snippet: Sfl1-mediated repression is important for FLO11 regulation but is absent in the 133d strain. (A) Northern blot analysis of FLO11 mRNA, as described in , for the indicated wild-type and mutant strains. (B) qRT-PCR analysis of FLO11 and SFL1 expression

    Article Snippet: For expression analysis by quantitative RT-PCR (qRT-PCR) cDNA was synthesized using the Transcriptor First Strand cDNA Synthesis Kit (Roche), and cDNA was quantitatively measured in triplicate with the ABI Prism 7000 sequence detection system. cDNA was used for normalization.

    Techniques: Northern Blot, Mutagenesis, Quantitative RT-PCR, Expressing

    Rpd3 counteracts the action of Sfl1 on the laboratory FLO11 allele by regulating ICR1 ncRNA. (A) Northern blot analysis of FLO11 mRNA, as described in , for the indicated wild-type and mutant strains. (B) qRT-PCR analysis of ICR1 ncRNA expression

    Journal: Genetics

    Article Title: Chromatin Modulation at the FLO11 Promoter of Saccharomyces cerevisiae by HDAC and Swi/Snf Complexes

    doi: 10.1534/genetics.112.140301

    Figure Lengend Snippet: Rpd3 counteracts the action of Sfl1 on the laboratory FLO11 allele by regulating ICR1 ncRNA. (A) Northern blot analysis of FLO11 mRNA, as described in , for the indicated wild-type and mutant strains. (B) qRT-PCR analysis of ICR1 ncRNA expression

    Article Snippet: For expression analysis by quantitative RT-PCR (qRT-PCR) cDNA was synthesized using the Transcriptor First Strand cDNA Synthesis Kit (Roche), and cDNA was quantitatively measured in triplicate with the ABI Prism 7000 sequence detection system. cDNA was used for normalization.

    Techniques: Northern Blot, Mutagenesis, Quantitative RT-PCR, Expressing

    Verification of RNA-seq results by qRT-PCR. The DEGs in GXU-34176 vs GXU-34140 related to the category of ‘abscisic acid-activated signaling pathway’ (c71654.graph_c0 and c65832.graph_c0), ‘leaf senescence’ (c64240.graph_c0), ‘response to ethylene’ (c67492.graph_c0) and ‘cell wall modification involved in abscission’ (c65986.graph_c0). The DEGs in GN18 vs FN95–1702 related to the category of ‘response to water deprivation’ (c54647.graph_c0, c56804.graph_c0 and c61335.graph_c0) and ‘response to oxidative stress’ (c57471.graph_c0). The DEGs in GUC2 vs GUC10 related to the category of ‘ubiquitin-protein transferase activity’ (c69746.graph_c0), ‘defense response to fungus’ (c72075.graph_c0), ‘response to jasmonic acid’ (c65355.graph_c0). Data of qRT-PCR are presented as mean ± SD (n = 9) and error bars represent SD.

    Journal: Scientific Reports

    Article Title: Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

    doi: 10.1038/s41598-018-19832-x

    Figure Lengend Snippet: Verification of RNA-seq results by qRT-PCR. The DEGs in GXU-34176 vs GXU-34140 related to the category of ‘abscisic acid-activated signaling pathway’ (c71654.graph_c0 and c65832.graph_c0), ‘leaf senescence’ (c64240.graph_c0), ‘response to ethylene’ (c67492.graph_c0) and ‘cell wall modification involved in abscission’ (c65986.graph_c0). The DEGs in GN18 vs FN95–1702 related to the category of ‘response to water deprivation’ (c54647.graph_c0, c56804.graph_c0 and c61335.graph_c0) and ‘response to oxidative stress’ (c57471.graph_c0). The DEGs in GUC2 vs GUC10 related to the category of ‘ubiquitin-protein transferase activity’ (c69746.graph_c0), ‘defense response to fungus’ (c72075.graph_c0), ‘response to jasmonic acid’ (c65355.graph_c0). Data of qRT-PCR are presented as mean ± SD (n = 9) and error bars represent SD.

    Article Snippet: qRT-PCR analysis qRT-PCR was carried out to validate the reliability of differentially expressed genes in the LightCycler 480 thermocycler (Roche).

    Techniques: RNA Sequencing Assay, Quantitative RT-PCR, Modification, Activity Assay