total rna extraction Search Results


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  • 98
    Jena Bioscience total rna extraction
    Total Rna Extraction, supplied by Jena Bioscience, used in various techniques. Bioz Stars score: 98/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Zymo Research total rna extraction
    Expression profiling of the human genes CYP27B1, METTL1, VDIR , and CYP24 . Quantitative real-time <t>PCR</t> was performed in order to study the relative mRNA expression levels of the genes CYP27B1, METTL1, VDIR and CYP24 in HEK-293 and MCF-7 cells and their responsiveness to 1α,25(OH) 2 D 3 over time ( A ). The cells were treated with 10 nM 1α,25(OH) 2 D 3 for 2, 6 and 24 h, prior to the extraction of <t>RNA.</t> The dependence of the hormone responsiveness of the genes on VDR expression was investigated by RNAi inhibition experiments. For this purpose, the cells were transfected with unspecific control siRNA oligomers or with specific siRNAs against the VDR mRNA. The siRNA treatment time was 72 h. Silencing of VDR at protein level was verified by immunoblotting using whole-cell extracts ( B ). After siRNA treatment, the cells were further treated with 10 nM 1α,25(OH) 2 D 3 for 3 h. The extracted RNA was reverse transcribed and analyzed by quantitative real-time PCR ( C ). Columns indicate the means of three independent cell treatments and the tips of the bars represent standard deviations. Two-tailed, paired Student's t -tests were performed and P -values (* P
    Total Rna Extraction, supplied by Zymo Research, used in various techniques. Bioz Stars score: 94/100, based on 204 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total rna extraction total rna extraction
    EBNA3C regulates Bcl6 mRNA expression through inhibition of its promoter activity. A) 5 million BJAB, BJAB7, BJAB10, LCL1 and LCL2 cells were harvested and extracted total <t>RNA</t> using <t>Trizol</t> reagent. Then cDNA was prepared with reverse transcriptase kit, and detected Bcl6 mRNA expression by quantitative Real-time PCR analysis (SYBR green). GAPDH was set as an internal reference. Each sample was determined in triplicate. B) EBNA3C knock-down (sh-E3C) stable LCL1 or control (sh-Ctrl) LCL1 cells were harvested and Bcl6 mRNA expression was detected using Real-time PCR as mentioned. C) 10 million BJAB10 cells were transfected with specific EBNA3C (sh-E3C) or control (sh-Ctrl) short hairpin RNA. At 48 hours post-transfection, total RNA was extracted, reverse-transcribed, followed by quantitative Real-time PCR analysis. Meanwhile, EBNA3C expression was also detected by western blot analysis. D) HEK293T cells were transfected with the reporter constructs containing wild-type Bcl6 promoter (pLA/B9) and increasing amount of Myc-EBNA3C. Cells were collected and lysed in lysis buffer at 48 hours post-transfection. Luciferase activity was measured according to the dual-luciferase reporter assay kit. Mean values and standard deviations of two independent experiments were presented. Cell lysate was resolved by 10% SDS-PAGE in order to check EBNA3C expression. GAPDH western blot was done as an internal loading control. E) HEK293T cells were transfected with wild-type Bcl6 promoter reporter plasmids in combination with different expression constructs as indicated. Cells were collected and lysed, then the lysate were used to detect luciferase activity as previously described.
    Total Rna Extraction Total Rna Extraction, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 206 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Toyobo total rna extraction kit
    EBNA3C regulates Bcl6 mRNA expression through inhibition of its promoter activity. A) 5 million BJAB, BJAB7, BJAB10, LCL1 and LCL2 cells were harvested and extracted total <t>RNA</t> using <t>Trizol</t> reagent. Then cDNA was prepared with reverse transcriptase kit, and detected Bcl6 mRNA expression by quantitative Real-time PCR analysis (SYBR green). GAPDH was set as an internal reference. Each sample was determined in triplicate. B) EBNA3C knock-down (sh-E3C) stable LCL1 or control (sh-Ctrl) LCL1 cells were harvested and Bcl6 mRNA expression was detected using Real-time PCR as mentioned. C) 10 million BJAB10 cells were transfected with specific EBNA3C (sh-E3C) or control (sh-Ctrl) short hairpin RNA. At 48 hours post-transfection, total RNA was extracted, reverse-transcribed, followed by quantitative Real-time PCR analysis. Meanwhile, EBNA3C expression was also detected by western blot analysis. D) HEK293T cells were transfected with the reporter constructs containing wild-type Bcl6 promoter (pLA/B9) and increasing amount of Myc-EBNA3C. Cells were collected and lysed in lysis buffer at 48 hours post-transfection. Luciferase activity was measured according to the dual-luciferase reporter assay kit. Mean values and standard deviations of two independent experiments were presented. Cell lysate was resolved by 10% SDS-PAGE in order to check EBNA3C expression. GAPDH western blot was done as an internal loading control. E) HEK293T cells were transfected with wild-type Bcl6 promoter reporter plasmids in combination with different expression constructs as indicated. Cells were collected and lysed, then the lysate were used to detect luciferase activity as previously described.
    Total Rna Extraction Kit, supplied by Toyobo, used in various techniques. Bioz Stars score: 90/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega total rna extraction kit
    RpoE1 regulates positively the expression of hrp gene cluster ( hrpA - F ), type III secreted effector-encoding genes ( XC_0241 and XC_1553 ) and the hrp master regulator hrpX . (A) Quantitative real-time PCR analysis of the transcription of hrpA - F, hrpG, hrpX, XC_0241 , and XC_1553 in the <t>Xcc</t> wild-type strain 8004 and the rpoE1 deletion mutant strain Δ rpoE1 . <t>RNA</t> was isolated from cultures of the strains grown in XCM1 medium for 24 h. The relative mRNA level was calculated with respect to the level of the corresponding transcript in the wild-type strain 8004. (B) GUS activity of hrpB, hrpF, hrpG, hrpX, XC_0241 , and XC_1553 promoter- gusA reporters (pLgushrpB, pLgushrpF, pLgushrpG, pLgushrpX, pLgus0241, and pLgus1553) in the wild-type strain 8004 and the mutant strain Δ rpoE1 . The strains were cultured in XCM1 medium for 24 h and GUS activity in the total culture was determined by using ρ-nitrophenyl-β-D-glucuronide as substrate. Values given are means ± standard deviations of triplicate measurements from a representative experiment; similar results were obtained in two other independent experiments. Asterisks indicate statistically significant difference, compared with the wild type (Student's t -test). ** P
    Total Rna Extraction Kit, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 257 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tiangen biotech co total rna extraction kit
    Real-time polymerase chain reaction detection of c-kit, <t>SCF,</t> and PI3K messenger <t>RNA</t> expression. The figure shows the representative result from repeated experiments ( n = 8). Data are expressed as mean ± standard deviation. Compared with Group A, ∗ P
    Total Rna Extraction Kit, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 93/100, based on 415 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GE Healthcare total rna extraction kit
    Real-time polymerase chain reaction detection of c-kit, <t>SCF,</t> and PI3K messenger <t>RNA</t> expression. The figure shows the representative result from repeated experiments ( n = 8). Data are expressed as mean ± standard deviation. Compared with Group A, ∗ P
    Total Rna Extraction Kit, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MACHEREY NAGEL total rna extraction kit
    Real-time polymerase chain reaction detection of c-kit, <t>SCF,</t> and PI3K messenger <t>RNA</t> expression. The figure shows the representative result from repeated experiments ( n = 8). Data are expressed as mean ± standard deviation. Compared with Group A, ∗ P
    Total Rna Extraction Kit, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen total rna extraction
    Distribution of exonic, intronic and intergenic reads in the six combinations of experiments. The barplot shows for each sequencing group the respective fraction (%) of the sum of aligned read of each replicate. Tri : TRIzol <t>RNA;</t> Qia : <t>Qiagen</t> RNA; RiboZ = RiboZero; Par = PARIS RNA extraction kit (Ambion); cyt : cytoplasm RNA; nuc : nuclear RNA.
    Total Rna Extraction, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 7087 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Vazyme Biotech Co total rna extraction reagent
    Distribution of exonic, intronic and intergenic reads in the six combinations of experiments. The barplot shows for each sequencing group the respective fraction (%) of the sum of aligned read of each replicate. Tri : TRIzol <t>RNA;</t> Qia : <t>Qiagen</t> RNA; RiboZ = RiboZero; Par = PARIS RNA extraction kit (Ambion); cyt : cytoplasm RNA; nuc : nuclear RNA.
    Total Rna Extraction Reagent, supplied by Vazyme Biotech Co, used in various techniques. Bioz Stars score: 90/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BioTek Instruments total rna extraction kit
    Distribution of exonic, intronic and intergenic reads in the six combinations of experiments. The barplot shows for each sequencing group the respective fraction (%) of the sum of aligned read of each replicate. Tri : TRIzol <t>RNA;</t> Qia : <t>Qiagen</t> RNA; RiboZ = RiboZero; Par = PARIS RNA extraction kit (Ambion); cyt : cytoplasm RNA; nuc : nuclear RNA.
    Total Rna Extraction Kit, supplied by BioTek Instruments, used in various techniques. Bioz Stars score: 92/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad total rna extraction
    Global organization and functionality of the newly identified 28-kb GI harboring β-myrcene core-code. ( A ) Genomic locus organization and functional elements detected using in silico prediction. Genes transcribed in forward orientation are represented by rightward arrows, whereas genes located in antisense strand are represented by leftward arrows. Genes are organized in TU, promoter regions (P) are illustrated by blue arrows, and terminator sites indicated by red circles. ( B ) Detailed analysis of the <t>RNA-seq</t> data mapping with the GI. In the top panel, read mapping coverage per base was plotted for samples derived from <t>M1</t> growth in lactate (gray line) and in β-myrcene (blue line). Prediction of the operon-like transcripts (horizontal orange bars) and transcription starting sites (TSS) (red arrows) was carried out with ReadXplorer ( Hilker et al. 2014 ). Expression levels for each gene are shown, in the bottom panel, as the ratio (FC) of normalized transcripts between cells grown in lactate (L) and cells grown in β-myrcene (M).
    Total Rna Extraction, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 92/100, based on 269 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total rna extract
    Global organization and functionality of the newly identified 28-kb GI harboring β-myrcene core-code. ( A ) Genomic locus organization and functional elements detected using in silico prediction. Genes transcribed in forward orientation are represented by rightward arrows, whereas genes located in antisense strand are represented by leftward arrows. Genes are organized in TU, promoter regions (P) are illustrated by blue arrows, and terminator sites indicated by red circles. ( B ) Detailed analysis of the <t>RNA-seq</t> data mapping with the GI. In the top panel, read mapping coverage per base was plotted for samples derived from <t>M1</t> growth in lactate (gray line) and in β-myrcene (blue line). Prediction of the operon-like transcripts (horizontal orange bars) and transcription starting sites (TSS) (red arrows) was carried out with ReadXplorer ( Hilker et al. 2014 ). Expression levels for each gene are shown, in the bottom panel, as the ratio (FC) of normalized transcripts between cells grown in lactate (L) and cells grown in β-myrcene (M).
    Total Rna Extract, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 146 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    iNtRON Biotechnology total rna extraction kit
    Relative expression of AtGA20ox gene in T 0 <t>transgenic</t> kenaf plants in three stages of their growth. Tissues were harvested at different phases of their growth as first (8–10 weeks), second (28–30 weeks) and third (after 30 weeks) phases and total <t>RNA</t> was amplified by real-time PCR using AtGA20ox sequence specific primers to measure the transcript level. Expression levels were normalised against 18S and 17S.
    Total Rna Extraction Kit, supplied by iNtRON Biotechnology, used in various techniques. Bioz Stars score: 92/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bioteke Corporation total rna extraction kit
    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear <t>RNA</t> and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P
    Total Rna Extraction Kit, supplied by Bioteke Corporation, used in various techniques. Bioz Stars score: 92/100, based on 118 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bioneer Corporation total rna extraction kit
    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear <t>RNA</t> and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P
    Total Rna Extraction Kit, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 91/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Norgen Biotek total rna extraction kit
    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear <t>RNA</t> and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P
    Total Rna Extraction Kit, supplied by Norgen Biotek, used in various techniques. Bioz Stars score: 90/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega total rna extraction system
    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear <t>RNA</t> and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P
    Total Rna Extraction System, supplied by Promega, used in various techniques. Bioz Stars score: 85/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Nanjing KeyGen Biotech Co Ltd total rna extraction kit
    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear <t>RNA</t> and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P
    Total Rna Extraction Kit, supplied by Nanjing KeyGen Biotech Co Ltd, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Macrogen total rna extraction kit
    The levels of GAMYB transcript were not upregulated in Koshihikari. Relative transcript levels of GAMYB in Nipponbare and Koshihikari ( a ), ZH11 and ZH11( el1 ) ( b ), and HNIL(M23) and HNIL(H143) ( c ), were normalized to the transcript levels of UBQ5 . The <t>RT-qPCR</t> was performed with total <t>RNA</t> from germinating seeds 2 days after soaking. Means and standard deviations were obtained from three replications. The experiments were repeated twice with similar results and Student’s t -test was used for statistical analysis (*** P
    Total Rna Extraction Kit, supplied by Macrogen, used in various techniques. Bioz Stars score: 92/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Omega Bio-tek total rna extraction kits
    The levels of GAMYB transcript were not upregulated in Koshihikari. Relative transcript levels of GAMYB in Nipponbare and Koshihikari ( a ), ZH11 and ZH11( el1 ) ( b ), and HNIL(M23) and HNIL(H143) ( c ), were normalized to the transcript levels of UBQ5 . The <t>RT-qPCR</t> was performed with total <t>RNA</t> from germinating seeds 2 days after soaking. Means and standard deviations were obtained from three replications. The experiments were repeated twice with similar results and Student’s t -test was used for statistical analysis (*** P
    Total Rna Extraction Kits, supplied by Omega Bio-tek, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Shanghai Generay Biotech total rna extraction kit
    Effect of p38 on the levels of <t>miR-155</t> and miR-99b, p65 expression and cytokine production. U937 and RAW264.7 cells were transfected with a control vector (indicated with NC), pcDNA3.1/p38 cDNA (indicated with p38), a nonspecific siRNA (indicated with sh-NC) or a specific siRNA directed against p38 (indicated with sh-p38). After 24 h post transfection, total <t>RNA</t> was extracted. miR-155 and miR-99b were detected via qRT-PCR. The results are representative of three independent experiments. Data are presented as the means ± SD. * P
    Total Rna Extraction Kit, supplied by Shanghai Generay Biotech, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Expression profiling of the human genes CYP27B1, METTL1, VDIR , and CYP24 . Quantitative real-time PCR was performed in order to study the relative mRNA expression levels of the genes CYP27B1, METTL1, VDIR and CYP24 in HEK-293 and MCF-7 cells and their responsiveness to 1α,25(OH) 2 D 3 over time ( A ). The cells were treated with 10 nM 1α,25(OH) 2 D 3 for 2, 6 and 24 h, prior to the extraction of RNA. The dependence of the hormone responsiveness of the genes on VDR expression was investigated by RNAi inhibition experiments. For this purpose, the cells were transfected with unspecific control siRNA oligomers or with specific siRNAs against the VDR mRNA. The siRNA treatment time was 72 h. Silencing of VDR at protein level was verified by immunoblotting using whole-cell extracts ( B ). After siRNA treatment, the cells were further treated with 10 nM 1α,25(OH) 2 D 3 for 3 h. The extracted RNA was reverse transcribed and analyzed by quantitative real-time PCR ( C ). Columns indicate the means of three independent cell treatments and the tips of the bars represent standard deviations. Two-tailed, paired Student's t -tests were performed and P -values (* P

    Journal: Nucleic Acids Research

    Article Title: Selective use of multiple vitamin D response elements underlies the 1 ?,25-dihydroxyvitamin D3-mediated negative regulation of the human CYP27B1 gene

    doi: 10.1093/nar/gkm179

    Figure Lengend Snippet: Expression profiling of the human genes CYP27B1, METTL1, VDIR , and CYP24 . Quantitative real-time PCR was performed in order to study the relative mRNA expression levels of the genes CYP27B1, METTL1, VDIR and CYP24 in HEK-293 and MCF-7 cells and their responsiveness to 1α,25(OH) 2 D 3 over time ( A ). The cells were treated with 10 nM 1α,25(OH) 2 D 3 for 2, 6 and 24 h, prior to the extraction of RNA. The dependence of the hormone responsiveness of the genes on VDR expression was investigated by RNAi inhibition experiments. For this purpose, the cells were transfected with unspecific control siRNA oligomers or with specific siRNAs against the VDR mRNA. The siRNA treatment time was 72 h. Silencing of VDR at protein level was verified by immunoblotting using whole-cell extracts ( B ). After siRNA treatment, the cells were further treated with 10 nM 1α,25(OH) 2 D 3 for 3 h. The extracted RNA was reverse transcribed and analyzed by quantitative real-time PCR ( C ). Columns indicate the means of three independent cell treatments and the tips of the bars represent standard deviations. Two-tailed, paired Student's t -tests were performed and P -values (* P

    Article Snippet: Total RNA extraction, cDNA synthesis and real-time PCR Total RNA was extracted using the Mini RNA Isolation II kit (Zymo Research, HiSS Diagnostics, Freiburg, Germany) and cDNA synthesis was performed for 1 h at 37°C using 1 µg of total RNA as a template, in the presence of 100 pmol oligodT18 primer and 40 U reverse transcriptase (Fermentas, Vilnius, Lithuania).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Inhibition, Transfection, Two Tailed Test

    EBNA3C regulates Bcl6 mRNA expression through inhibition of its promoter activity. A) 5 million BJAB, BJAB7, BJAB10, LCL1 and LCL2 cells were harvested and extracted total RNA using Trizol reagent. Then cDNA was prepared with reverse transcriptase kit, and detected Bcl6 mRNA expression by quantitative Real-time PCR analysis (SYBR green). GAPDH was set as an internal reference. Each sample was determined in triplicate. B) EBNA3C knock-down (sh-E3C) stable LCL1 or control (sh-Ctrl) LCL1 cells were harvested and Bcl6 mRNA expression was detected using Real-time PCR as mentioned. C) 10 million BJAB10 cells were transfected with specific EBNA3C (sh-E3C) or control (sh-Ctrl) short hairpin RNA. At 48 hours post-transfection, total RNA was extracted, reverse-transcribed, followed by quantitative Real-time PCR analysis. Meanwhile, EBNA3C expression was also detected by western blot analysis. D) HEK293T cells were transfected with the reporter constructs containing wild-type Bcl6 promoter (pLA/B9) and increasing amount of Myc-EBNA3C. Cells were collected and lysed in lysis buffer at 48 hours post-transfection. Luciferase activity was measured according to the dual-luciferase reporter assay kit. Mean values and standard deviations of two independent experiments were presented. Cell lysate was resolved by 10% SDS-PAGE in order to check EBNA3C expression. GAPDH western blot was done as an internal loading control. E) HEK293T cells were transfected with wild-type Bcl6 promoter reporter plasmids in combination with different expression constructs as indicated. Cells were collected and lysed, then the lysate were used to detect luciferase activity as previously described.

    Journal: PLoS Pathogens

    Article Title: An essential EBV latent antigen 3C binds Bcl6 for targeted degradation and cell proliferation

    doi: 10.1371/journal.ppat.1006500

    Figure Lengend Snippet: EBNA3C regulates Bcl6 mRNA expression through inhibition of its promoter activity. A) 5 million BJAB, BJAB7, BJAB10, LCL1 and LCL2 cells were harvested and extracted total RNA using Trizol reagent. Then cDNA was prepared with reverse transcriptase kit, and detected Bcl6 mRNA expression by quantitative Real-time PCR analysis (SYBR green). GAPDH was set as an internal reference. Each sample was determined in triplicate. B) EBNA3C knock-down (sh-E3C) stable LCL1 or control (sh-Ctrl) LCL1 cells were harvested and Bcl6 mRNA expression was detected using Real-time PCR as mentioned. C) 10 million BJAB10 cells were transfected with specific EBNA3C (sh-E3C) or control (sh-Ctrl) short hairpin RNA. At 48 hours post-transfection, total RNA was extracted, reverse-transcribed, followed by quantitative Real-time PCR analysis. Meanwhile, EBNA3C expression was also detected by western blot analysis. D) HEK293T cells were transfected with the reporter constructs containing wild-type Bcl6 promoter (pLA/B9) and increasing amount of Myc-EBNA3C. Cells were collected and lysed in lysis buffer at 48 hours post-transfection. Luciferase activity was measured according to the dual-luciferase reporter assay kit. Mean values and standard deviations of two independent experiments were presented. Cell lysate was resolved by 10% SDS-PAGE in order to check EBNA3C expression. GAPDH western blot was done as an internal loading control. E) HEK293T cells were transfected with wild-type Bcl6 promoter reporter plasmids in combination with different expression constructs as indicated. Cells were collected and lysed, then the lysate were used to detect luciferase activity as previously described.

    Article Snippet: Then total RNA extraction was performed using Trizol reagent (Invitrogen, Inc., Carlsbad, CA) and treated with Dnase I (Invitrogen, Inc., Carlsbad, CA), then cDNA was prepared with Superscript II reverse transcriptase kit (Invitrogen, Inc., Carlsbad, CA) according to the manufacturer’s protocol.

    Techniques: Expressing, Inhibition, Activity Assay, Real-time Polymerase Chain Reaction, SYBR Green Assay, Transfection, shRNA, Western Blot, Construct, Proximity Ligation Assay, Lysis, Luciferase, Reporter Assay, SDS Page

    RpoE1 regulates positively the expression of hrp gene cluster ( hrpA - F ), type III secreted effector-encoding genes ( XC_0241 and XC_1553 ) and the hrp master regulator hrpX . (A) Quantitative real-time PCR analysis of the transcription of hrpA - F, hrpG, hrpX, XC_0241 , and XC_1553 in the Xcc wild-type strain 8004 and the rpoE1 deletion mutant strain Δ rpoE1 . RNA was isolated from cultures of the strains grown in XCM1 medium for 24 h. The relative mRNA level was calculated with respect to the level of the corresponding transcript in the wild-type strain 8004. (B) GUS activity of hrpB, hrpF, hrpG, hrpX, XC_0241 , and XC_1553 promoter- gusA reporters (pLgushrpB, pLgushrpF, pLgushrpG, pLgushrpX, pLgus0241, and pLgus1553) in the wild-type strain 8004 and the mutant strain Δ rpoE1 . The strains were cultured in XCM1 medium for 24 h and GUS activity in the total culture was determined by using ρ-nitrophenyl-β-D-glucuronide as substrate. Values given are means ± standard deviations of triplicate measurements from a representative experiment; similar results were obtained in two other independent experiments. Asterisks indicate statistically significant difference, compared with the wild type (Student's t -test). ** P

    Journal: Frontiers in Microbiology

    Article Title: Systematic Functional Analysis of Sigma (σ) Factors in the Phytopathogen Xanthomonas campestris Reveals Novel Roles in the Regulation of Virulence and Viability

    doi: 10.3389/fmicb.2018.01749

    Figure Lengend Snippet: RpoE1 regulates positively the expression of hrp gene cluster ( hrpA - F ), type III secreted effector-encoding genes ( XC_0241 and XC_1553 ) and the hrp master regulator hrpX . (A) Quantitative real-time PCR analysis of the transcription of hrpA - F, hrpG, hrpX, XC_0241 , and XC_1553 in the Xcc wild-type strain 8004 and the rpoE1 deletion mutant strain Δ rpoE1 . RNA was isolated from cultures of the strains grown in XCM1 medium for 24 h. The relative mRNA level was calculated with respect to the level of the corresponding transcript in the wild-type strain 8004. (B) GUS activity of hrpB, hrpF, hrpG, hrpX, XC_0241 , and XC_1553 promoter- gusA reporters (pLgushrpB, pLgushrpF, pLgushrpG, pLgushrpX, pLgus0241, and pLgus1553) in the wild-type strain 8004 and the mutant strain Δ rpoE1 . The strains were cultured in XCM1 medium for 24 h and GUS activity in the total culture was determined by using ρ-nitrophenyl-β-D-glucuronide as substrate. Values given are means ± standard deviations of triplicate measurements from a representative experiment; similar results were obtained in two other independent experiments. Asterisks indicate statistically significant difference, compared with the wild type (Student's t -test). ** P

    Article Snippet: The total RNA of Xcc strains was extracted with a total-RNA extraction kit (Promega, Madison, Wisconsin, USA) and reverse transcription was performed using a cDNA synthesis kit (Takara, Dalian, China), according to the manufacturer's instructions.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Mutagenesis, Isolation, Activity Assay, Cell Culture

    RpoE1 enhances the expression of hrpX in vivo and in vitro . (A) Quantitative real-time PCR (qRT-PCR) showed that overexpression of RpoE1 in Xcc enhanced hrpX transcription. For the qRT-PCR, Xcc wild-type strain 8004 and its derivative strain 8004/pJrpoE1 which overexpresses RpoE1 in the wild-type background were grown in the minimal medium XCM1. RNA was isolated from the cultures after incubation for 24 h. The relative mRNA level of hrpX was analyzed by qRT-PCR and calculated with respect to the transcript level in strain 8004. Data are means ± standard deviations of triplicate measurements from a representative experiment; similar results were obtained in two other independent experiments. Asterisks indicate statistically significant difference (Student's t -test). ** P

    Journal: Frontiers in Microbiology

    Article Title: Systematic Functional Analysis of Sigma (σ) Factors in the Phytopathogen Xanthomonas campestris Reveals Novel Roles in the Regulation of Virulence and Viability

    doi: 10.3389/fmicb.2018.01749

    Figure Lengend Snippet: RpoE1 enhances the expression of hrpX in vivo and in vitro . (A) Quantitative real-time PCR (qRT-PCR) showed that overexpression of RpoE1 in Xcc enhanced hrpX transcription. For the qRT-PCR, Xcc wild-type strain 8004 and its derivative strain 8004/pJrpoE1 which overexpresses RpoE1 in the wild-type background were grown in the minimal medium XCM1. RNA was isolated from the cultures after incubation for 24 h. The relative mRNA level of hrpX was analyzed by qRT-PCR and calculated with respect to the transcript level in strain 8004. Data are means ± standard deviations of triplicate measurements from a representative experiment; similar results were obtained in two other independent experiments. Asterisks indicate statistically significant difference (Student's t -test). ** P

    Article Snippet: The total RNA of Xcc strains was extracted with a total-RNA extraction kit (Promega, Madison, Wisconsin, USA) and reverse transcription was performed using a cDNA synthesis kit (Takara, Dalian, China), according to the manufacturer's instructions.

    Techniques: Expressing, In Vivo, In Vitro, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Over Expression, Isolation, Incubation

    Real-time polymerase chain reaction detection of c-kit, SCF, and PI3K messenger RNA expression. The figure shows the representative result from repeated experiments ( n = 8). Data are expressed as mean ± standard deviation. Compared with Group A, ∗ P

    Journal: Evidence-based Complementary and Alternative Medicine : eCAM

    Article Title: Aqueous Extracts of Herba Cistanche Promoted Intestinal Motility in Loperamide-Induced Constipation Rats by Ameliorating the Interstitial Cells of Cajal

    doi: 10.1155/2017/6236904

    Figure Lengend Snippet: Real-time polymerase chain reaction detection of c-kit, SCF, and PI3K messenger RNA expression. The figure shows the representative result from repeated experiments ( n = 8). Data are expressed as mean ± standard deviation. Compared with Group A, ∗ P

    Article Snippet: Real-Time Polymerase Chain Reaction Gene expression levels of c-kit, SCF, and PI3K mRNAs in the colon were determined using a total RNA extraction kit (TIANGEN Biotech, Beijing, China) according to the manufacturer's protocols.

    Techniques: Real-time Polymerase Chain Reaction, RNA Expression, Standard Deviation

    Distribution of exonic, intronic and intergenic reads in the six combinations of experiments. The barplot shows for each sequencing group the respective fraction (%) of the sum of aligned read of each replicate. Tri : TRIzol RNA; Qia : Qiagen RNA; RiboZ = RiboZero; Par = PARIS RNA extraction kit (Ambion); cyt : cytoplasm RNA; nuc : nuclear RNA.

    Journal: BMC Genomics

    Article Title: Influence of RNA extraction methods and library selection schemes on RNA-seq data

    doi: 10.1186/1471-2164-15-675

    Figure Lengend Snippet: Distribution of exonic, intronic and intergenic reads in the six combinations of experiments. The barplot shows for each sequencing group the respective fraction (%) of the sum of aligned read of each replicate. Tri : TRIzol RNA; Qia : Qiagen RNA; RiboZ = RiboZero; Par = PARIS RNA extraction kit (Ambion); cyt : cytoplasm RNA; nuc : nuclear RNA.

    Article Snippet: Qiagen total RNA extraction (RNA3, 4) Total RNA from cell pellets was purified using the RNeasy Mini Kit (Qiagen, #74104) and frozen cells were re-suspended in 350 μl of buffer RLT and the lysates were passed 5 times through a 20-gauge needle, and processed following the manufacturer’s instructions.

    Techniques: Sequencing, RNA Extraction

    BRAF gene coverage. Snap shot (UCSC browser) representing the normalized read coverage for each method and the protocol dependence of the intronic reads. From top to bottom the experimental groups are the following: Poly (A) Qiagen total RNA, Poly (A) TRIzol total RNA, RiboZero Qiagen total RNA, RiboZero TRIzol total RNA, RiboZero cytoplasmic RNA, RiboZero nuclear RNA.

    Journal: BMC Genomics

    Article Title: Influence of RNA extraction methods and library selection schemes on RNA-seq data

    doi: 10.1186/1471-2164-15-675

    Figure Lengend Snippet: BRAF gene coverage. Snap shot (UCSC browser) representing the normalized read coverage for each method and the protocol dependence of the intronic reads. From top to bottom the experimental groups are the following: Poly (A) Qiagen total RNA, Poly (A) TRIzol total RNA, RiboZero Qiagen total RNA, RiboZero TRIzol total RNA, RiboZero cytoplasmic RNA, RiboZero nuclear RNA.

    Article Snippet: Qiagen total RNA extraction (RNA3, 4) Total RNA from cell pellets was purified using the RNeasy Mini Kit (Qiagen, #74104) and frozen cells were re-suspended in 350 μl of buffer RLT and the lysates were passed 5 times through a 20-gauge needle, and processed following the manufacturer’s instructions.

    Techniques:

    Global organization and functionality of the newly identified 28-kb GI harboring β-myrcene core-code. ( A ) Genomic locus organization and functional elements detected using in silico prediction. Genes transcribed in forward orientation are represented by rightward arrows, whereas genes located in antisense strand are represented by leftward arrows. Genes are organized in TU, promoter regions (P) are illustrated by blue arrows, and terminator sites indicated by red circles. ( B ) Detailed analysis of the RNA-seq data mapping with the GI. In the top panel, read mapping coverage per base was plotted for samples derived from M1 growth in lactate (gray line) and in β-myrcene (blue line). Prediction of the operon-like transcripts (horizontal orange bars) and transcription starting sites (TSS) (red arrows) was carried out with ReadXplorer ( Hilker et al. 2014 ). Expression levels for each gene are shown, in the bottom panel, as the ratio (FC) of normalized transcripts between cells grown in lactate (L) and cells grown in β-myrcene (M).

    Journal: Genome Biology and Evolution

    Article Title: Deciphering the Genome Repertoire of Pseudomonas sp. M1 toward β-Myrcene Biotransformation

    doi: 10.1093/gbe/evu254

    Figure Lengend Snippet: Global organization and functionality of the newly identified 28-kb GI harboring β-myrcene core-code. ( A ) Genomic locus organization and functional elements detected using in silico prediction. Genes transcribed in forward orientation are represented by rightward arrows, whereas genes located in antisense strand are represented by leftward arrows. Genes are organized in TU, promoter regions (P) are illustrated by blue arrows, and terminator sites indicated by red circles. ( B ) Detailed analysis of the RNA-seq data mapping with the GI. In the top panel, read mapping coverage per base was plotted for samples derived from M1 growth in lactate (gray line) and in β-myrcene (blue line). Prediction of the operon-like transcripts (horizontal orange bars) and transcription starting sites (TSS) (red arrows) was carried out with ReadXplorer ( Hilker et al. 2014 ). Expression levels for each gene are shown, in the bottom panel, as the ratio (FC) of normalized transcripts between cells grown in lactate (L) and cells grown in β-myrcene (M).

    Article Snippet: Total RNA Extraction from Pseudomonas sp. M1 Total RNA samples were obtained using the Aurum Total RNA Mini kit (Bio-Rad), as described by the manufacturer’s instructions.

    Techniques: Functional Assay, In Silico, RNA Sequencing Assay, Derivative Assay, Expressing

    Relative expression of AtGA20ox gene in T 0 transgenic kenaf plants in three stages of their growth. Tissues were harvested at different phases of their growth as first (8–10 weeks), second (28–30 weeks) and third (after 30 weeks) phases and total RNA was amplified by real-time PCR using AtGA20ox sequence specific primers to measure the transcript level. Expression levels were normalised against 18S and 17S.

    Journal: Breeding Science

    Article Title: Overexpression of Arabidopsis thaliana gibberellic acid 20 oxidase (AtGA20ox) gene enhance the vegetative growth and fiber quality in kenaf (Hibiscus cannabinus L.) plants

    doi: 10.1270/jsbbs.65.177

    Figure Lengend Snippet: Relative expression of AtGA20ox gene in T 0 transgenic kenaf plants in three stages of their growth. Tissues were harvested at different phases of their growth as first (8–10 weeks), second (28–30 weeks) and third (after 30 weeks) phases and total RNA was amplified by real-time PCR using AtGA20ox sequence specific primers to measure the transcript level. Expression levels were normalised against 18S and 17S.

    Article Snippet: Expression analysis of AtGA20ox gene in transgenic plants by real-time PCR Total RNA was extracted using total RNA extraction kit the easy-BLUE (iNtRON Biotechnology, Inc, Korea) from kenaf.

    Techniques: Expressing, Transgenic Assay, Amplification, Real-time Polymerase Chain Reaction, Sequencing

    miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear RNA and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P

    Journal: Experimental and Therapeutic Medicine

    Article Title: MicroRNA-210 contributes to peripheral nerve regeneration through promoting the proliferation and migration of Schwann cells

    doi: 10.3892/etm.2017.4869

    Figure Lengend Snippet: miR-210 levels in the proximal stump of the nerve. Levels of miR-210 in the sciatic nerve injury group and the sham group were detected by reverse-transcription quantitative polymerase chain reaction. The miR-210 level was normalized to U6 small nuclear RNA and the relative miR-210 level was calculated using the 2 −ΔΔCq method. Values are expressed as the mean ± standard deviation. ***P

    Article Snippet: RT-qPCR Total RNA was extracted from each sample using a total RNA extraction kit (BioTeke, Beijing, China) according to the manufacturer's protocol.

    Techniques: Real-time Polymerase Chain Reaction, Standard Deviation

    The levels of GAMYB transcript were not upregulated in Koshihikari. Relative transcript levels of GAMYB in Nipponbare and Koshihikari ( a ), ZH11 and ZH11( el1 ) ( b ), and HNIL(M23) and HNIL(H143) ( c ), were normalized to the transcript levels of UBQ5 . The RT-qPCR was performed with total RNA from germinating seeds 2 days after soaking. Means and standard deviations were obtained from three replications. The experiments were repeated twice with similar results and Student’s t -test was used for statistical analysis (*** P

    Journal: Rice

    Article Title: The Rice Floral Repressor Early flowering1 Affects Spikelet Fertility By Modulating Gibberellin Signaling

    doi: 10.1186/s12284-015-0058-1

    Figure Lengend Snippet: The levels of GAMYB transcript were not upregulated in Koshihikari. Relative transcript levels of GAMYB in Nipponbare and Koshihikari ( a ), ZH11 and ZH11( el1 ) ( b ), and HNIL(M23) and HNIL(H143) ( c ), were normalized to the transcript levels of UBQ5 . The RT-qPCR was performed with total RNA from germinating seeds 2 days after soaking. Means and standard deviations were obtained from three replications. The experiments were repeated twice with similar results and Student’s t -test was used for statistical analysis (*** P

    Article Snippet: Reverse Transcription And Quantitative Real-Time PCR (RT-qPCR) Total RNA from spikelets or germinating seeds was extracted using the Total RNA Extraction Kit (Macrogen, Korea).

    Techniques: Quantitative RT-PCR

    Up-regulation of GAMYB and pollen formation-related genes in the spikelets of HNIL(H143). Relative transcript levels of GAMYB ( a ), CYP703A3 ( Cytochrome P450 hydroxylase ) ( b ), KAR (β -ketoacyl reductase ) ( c ) in HNIL(M23) and HNIL(H143) spikelets were normalized to the transcript levels of UBQ5 . The RT-qPCR was performed with total RNA from spikelets at heading stage. The data were obtained from three independent biological replicates. Reactions were repeated at least twice. Student’s t -test was used for statistical analysis (*** P

    Journal: Rice

    Article Title: The Rice Floral Repressor Early flowering1 Affects Spikelet Fertility By Modulating Gibberellin Signaling

    doi: 10.1186/s12284-015-0058-1

    Figure Lengend Snippet: Up-regulation of GAMYB and pollen formation-related genes in the spikelets of HNIL(H143). Relative transcript levels of GAMYB ( a ), CYP703A3 ( Cytochrome P450 hydroxylase ) ( b ), KAR (β -ketoacyl reductase ) ( c ) in HNIL(M23) and HNIL(H143) spikelets were normalized to the transcript levels of UBQ5 . The RT-qPCR was performed with total RNA from spikelets at heading stage. The data were obtained from three independent biological replicates. Reactions were repeated at least twice. Student’s t -test was used for statistical analysis (*** P

    Article Snippet: Reverse Transcription And Quantitative Real-Time PCR (RT-qPCR) Total RNA from spikelets or germinating seeds was extracted using the Total RNA Extraction Kit (Macrogen, Korea).

    Techniques: Quantitative RT-PCR

    Effect of p38 on the levels of miR-155 and miR-99b, p65 expression and cytokine production. U937 and RAW264.7 cells were transfected with a control vector (indicated with NC), pcDNA3.1/p38 cDNA (indicated with p38), a nonspecific siRNA (indicated with sh-NC) or a specific siRNA directed against p38 (indicated with sh-p38). After 24 h post transfection, total RNA was extracted. miR-155 and miR-99b were detected via qRT-PCR. The results are representative of three independent experiments. Data are presented as the means ± SD. * P

    Journal: Emerging Microbes & Infections

    Article Title: Rv2346c enhances mycobacterial survival within macrophages by inhibiting TNF-α and IL-6 production via the p38/miRNA/NF-κB pathway

    doi: 10.1038/s41426-018-0162-6

    Figure Lengend Snippet: Effect of p38 on the levels of miR-155 and miR-99b, p65 expression and cytokine production. U937 and RAW264.7 cells were transfected with a control vector (indicated with NC), pcDNA3.1/p38 cDNA (indicated with p38), a nonspecific siRNA (indicated with sh-NC) or a specific siRNA directed against p38 (indicated with sh-p38). After 24 h post transfection, total RNA was extracted. miR-155 and miR-99b were detected via qRT-PCR. The results are representative of three independent experiments. Data are presented as the means ± SD. * P

    Article Snippet: Total RNA for miR-99b, miR-155, and U6 detection was extracted with a Total RNA Extraction Kit.

    Techniques: Expressing, Transfection, Plasmid Preparation, Quantitative RT-PCR

    Effect of Rv2346c on cytokine production, p65 expression, p38 phosphorylation, and miR-155 and miR-99b levels. U937 and RAW264.7 cells were infected with BCG (MOI 1/5) and cells in the BCG + Rv2346c groups were also treated with Rv2346c (500 pg/ml). After incubating for 24, 48, or 72 h, cell culture supernatants were collected and examined using ELISA assay ( a – d ); total protein was extracted and estimated via western blot ( e , f , g , i , j , k ); total RNA was extracted and analyzed via qRT-PCR ( h , l , m – p ). GAPDH and p38 were used as loading controls for protein expression analysis. Protein bands were scanned and the intensity was determined. The results are representative of three independent experiments. Data are presented as the means ± SD. * P

    Journal: Emerging Microbes & Infections

    Article Title: Rv2346c enhances mycobacterial survival within macrophages by inhibiting TNF-α and IL-6 production via the p38/miRNA/NF-κB pathway

    doi: 10.1038/s41426-018-0162-6

    Figure Lengend Snippet: Effect of Rv2346c on cytokine production, p65 expression, p38 phosphorylation, and miR-155 and miR-99b levels. U937 and RAW264.7 cells were infected with BCG (MOI 1/5) and cells in the BCG + Rv2346c groups were also treated with Rv2346c (500 pg/ml). After incubating for 24, 48, or 72 h, cell culture supernatants were collected and examined using ELISA assay ( a – d ); total protein was extracted and estimated via western blot ( e , f , g , i , j , k ); total RNA was extracted and analyzed via qRT-PCR ( h , l , m – p ). GAPDH and p38 were used as loading controls for protein expression analysis. Protein bands were scanned and the intensity was determined. The results are representative of three independent experiments. Data are presented as the means ± SD. * P

    Article Snippet: Total RNA for miR-99b, miR-155, and U6 detection was extracted with a Total RNA Extraction Kit.

    Techniques: Expressing, Infection, Cell Culture, Enzyme-linked Immunosorbent Assay, Western Blot, Quantitative RT-PCR