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    Thermo Fisher stepone real time pcr system
    Amplification curves obtained by β 0 39 or β + IVSI-110 genotyping assays from circulating DNA extracted from maternal plasma. Real-time <t>PCR</t> with β 0 39 (A) or β + IVSI-110 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels) were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β 0 39 (A) or β + IVSI-110 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. In panel (B), #146a and #146b refer to samples collected from the same pregnant woman (number 146) at different gestational ages: 5 weeks and 10 weeks, respectively. The amplification was performed by using the <t>StepOne</t> ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).
    Stepone Real Time Pcr System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 26526 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/stepone real time pcr system/product/Thermo Fisher
    Average 99 stars, based on 26526 article reviews
    Price from $9.99 to $1999.99
    stepone real time pcr system - by Bioz Stars, 2020-09
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    94
    Thermo Fisher abi stepone real time pcr system
    Amplification curves obtained by β 0 39 or β + IVSI-110 genotyping assays from circulating DNA extracted from maternal plasma. Real-time <t>PCR</t> with β 0 39 (A) or β + IVSI-110 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels) were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β 0 39 (A) or β + IVSI-110 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. In panel (B), #146a and #146b refer to samples collected from the same pregnant woman (number 146) at different gestational ages: 5 weeks and 10 weeks, respectively. The amplification was performed by using the <t>StepOne</t> ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).
    Abi Stepone Real Time Pcr System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 2205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/abi stepone real time pcr system/product/Thermo Fisher
    Average 94 stars, based on 2205 article reviews
    Price from $9.99 to $1999.99
    abi stepone real time pcr system - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    89
    Thermo Fisher stepone plus real time pcr instrument
    Amplification curves obtained by β 0 39 or β + IVSI-110 genotyping assays from circulating DNA extracted from maternal plasma. Real-time <t>PCR</t> with β 0 39 (A) or β + IVSI-110 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels) were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β 0 39 (A) or β + IVSI-110 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. In panel (B), #146a and #146b refer to samples collected from the same pregnant woman (number 146) at different gestational ages: 5 weeks and 10 weeks, respectively. The amplification was performed by using the <t>StepOne</t> ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).
    Stepone Plus Real Time Pcr Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 476 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/stepone plus real time pcr instrument/product/Thermo Fisher
    Average 89 stars, based on 476 article reviews
    Price from $9.99 to $1999.99
    stepone plus real time pcr instrument - by Bioz Stars, 2020-09
    89/100 stars
      Buy from Supplier

    Image Search Results


    Amplification curves obtained by β 0 39 or β + IVSI-110 genotyping assays from circulating DNA extracted from maternal plasma. Real-time PCR with β 0 39 (A) or β + IVSI-110 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels) were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β 0 39 (A) or β + IVSI-110 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. In panel (B), #146a and #146b refer to samples collected from the same pregnant woman (number 146) at different gestational ages: 5 weeks and 10 weeks, respectively. The amplification was performed by using the StepOne ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).

    Journal: PLoS ONE

    Article Title: Postnatal and non-invasive prenatal detection of β-thalassemia mutations based on Taqman genotyping assays

    doi: 10.1371/journal.pone.0172756

    Figure Lengend Snippet: Amplification curves obtained by β 0 39 or β + IVSI-110 genotyping assays from circulating DNA extracted from maternal plasma. Real-time PCR with β 0 39 (A) or β + IVSI-110 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels) were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β 0 39 (A) or β + IVSI-110 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. In panel (B), #146a and #146b refer to samples collected from the same pregnant woman (number 146) at different gestational ages: 5 weeks and 10 weeks, respectively. The amplification was performed by using the StepOne ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).

    Article Snippet: The reactions were carried out on a StepOne™ Real-Time PCR System (Applied Biosystems® —Thermo Fisher Scientific), by using the StepOne Software (Applied Biosystems® —Thermo Fisher Scientific).

    Techniques: Amplification, Real-time Polymerase Chain Reaction, Mutagenesis

    Amplification curves obtained by β + IVSI-6 or β 0 IVSI-1 genotyping assays from circulating DNA extracted from maternal plasma. Real-time PCR with β + IVSI-6 (A) or β 0 IVSI-1 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels), were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β + IVSI-6 (A) or β 0 IVSI-1 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. The amplification was performed by using the StepOne ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).

    Journal: PLoS ONE

    Article Title: Postnatal and non-invasive prenatal detection of β-thalassemia mutations based on Taqman genotyping assays

    doi: 10.1371/journal.pone.0172756

    Figure Lengend Snippet: Amplification curves obtained by β + IVSI-6 or β 0 IVSI-1 genotyping assays from circulating DNA extracted from maternal plasma. Real-time PCR with β + IVSI-6 (A) or β 0 IVSI-1 (B) genotyping assays, containing a normal probe (VIC ® , upper panels) and a mutated probe (FAM ™ , lower panels), were performed for circulating DNA extracted from maternal plasma where the father was a carrier of β + IVSI-6 (A) or β 0 IVSI-1 (B) thalassemia mutation, respectively. The plots show the ΔRn values as a function of the number of amplification cycles, while the threshold line is drawn in blue. Samples are listed according to increasing gestational ages. The amplification was performed by using the StepOne ™ Real-Time PCR System (Applied Biosystems ® —Thermo Fisher Scientific).

    Article Snippet: The reactions were carried out on a StepOne™ Real-Time PCR System (Applied Biosystems® —Thermo Fisher Scientific), by using the StepOne Software (Applied Biosystems® —Thermo Fisher Scientific).

    Techniques: Amplification, Real-time Polymerase Chain Reaction, Mutagenesis

    Tri6 auto-regulates its own expression in nutrient-rich conditions. A ) Arrangement of the Tri6 gene and location of Tri6 primers used in the RT-qPCR analysis of wildtype ( Wt ) and transgenic strains. The solid vertical box indicates the location of Tri6-ORF primers in the coding region of Tri6 (Filled horizontal box) of the wildtype and the Tri6 over-expressing transgenic strains ( tri6 Δ Tri6 ). The dotted vertical box indicates the location of Tri6 5′ UTR primers in the wildtype ( Wt ), the Tri6 mutant ( tri6 Δand the Tri6 over-expressing transgenic strains ( tri6 Δ Tri6 ). The location of the Hygromycin gene within the Tri6 coding region of the tri6 Δstrain ( tri6 Δis indicated by the striped horizontal box. Gpd indicates the promoter used to over-express Tri6 [41] . The solid horizontal lines indicate 5′ and 3′ flanking regions of the Tri6 gene. B ) The quantitative real-time PCR (RT-qPCR) analysis of Tri genes in wildtype, tri6 Δand the tri6 Δ Tri6 strains grown in nutrient-rich conditions. RT-qPCR reactions were performed in triplicates using Applied Biosystems Power SYBR Green kit and the Applied Biosystems Step One Plus Real-Time PCR System. A list of qPCR primers for all the Tri genes is listed in the Table S2 . The β-tubulin gene ( FGSG_09530 ) was used as the internal control and the data was imported and Relative quantity (RQ) was derived by the Relative standard method included in the StepOne 2.1 software. C ) Identical to B ), except the internal control used was Gapdh ( FGSG_06257 ). The figures are representative of two independent biological replicates.

    Journal: PLoS Pathogens

    Article Title: Tri6 Is a Global Transcription Regulator in the Phytopathogen Fusarium graminearum

    doi: 10.1371/journal.ppat.1002266

    Figure Lengend Snippet: Tri6 auto-regulates its own expression in nutrient-rich conditions. A ) Arrangement of the Tri6 gene and location of Tri6 primers used in the RT-qPCR analysis of wildtype ( Wt ) and transgenic strains. The solid vertical box indicates the location of Tri6-ORF primers in the coding region of Tri6 (Filled horizontal box) of the wildtype and the Tri6 over-expressing transgenic strains ( tri6 Δ Tri6 ). The dotted vertical box indicates the location of Tri6 5′ UTR primers in the wildtype ( Wt ), the Tri6 mutant ( tri6 Δand the Tri6 over-expressing transgenic strains ( tri6 Δ Tri6 ). The location of the Hygromycin gene within the Tri6 coding region of the tri6 Δstrain ( tri6 Δis indicated by the striped horizontal box. Gpd indicates the promoter used to over-express Tri6 [41] . The solid horizontal lines indicate 5′ and 3′ flanking regions of the Tri6 gene. B ) The quantitative real-time PCR (RT-qPCR) analysis of Tri genes in wildtype, tri6 Δand the tri6 Δ Tri6 strains grown in nutrient-rich conditions. RT-qPCR reactions were performed in triplicates using Applied Biosystems Power SYBR Green kit and the Applied Biosystems Step One Plus Real-Time PCR System. A list of qPCR primers for all the Tri genes is listed in the Table S2 . The β-tubulin gene ( FGSG_09530 ) was used as the internal control and the data was imported and Relative quantity (RQ) was derived by the Relative standard method included in the StepOne 2.1 software. C ) Identical to B ), except the internal control used was Gapdh ( FGSG_06257 ). The figures are representative of two independent biological replicates.

    Article Snippet: RT-qPCR was performed using the Applied Biosystems StepOne Plus Real Time PCR system (ABI, Foster City, USA).

    Techniques: Expressing, Quantitative RT-PCR, Transgenic Assay, Mutagenesis, Real-time Polymerase Chain Reaction, SYBR Green Assay, Derivative Assay, Software

    Relative mRNA expression level of IL-6, serotonin 2A receptor (5-HTR2A), serotonin 2C receptor (5-HTR2C), serotonin 6 receptor (5-HTR6) and serotonin 7 receptor (5-HTR7) in the brains of healthy or T. gondii -infected mice. Gene expression was detected by quantitative real-time PCR. β-Actin was used as a reference gene. The gene-specific primers are listed in the Material and Methods. The relative expression levels were calculated by the 2 (-ΔΔCT) method. Statistical analysis was performed using a one-way analysis of variance and Tukey's multiple comparison test. The values represent means ± S.D. ***p

    Journal: Heliyon

    Article Title: Expression of serotonin 2A, 2C, 6 and 7 receptor and IL-6 mRNA in experimental toxoplasmic encephalitis in mice

    doi: 10.1016/j.heliyon.2019.e02890

    Figure Lengend Snippet: Relative mRNA expression level of IL-6, serotonin 2A receptor (5-HTR2A), serotonin 2C receptor (5-HTR2C), serotonin 6 receptor (5-HTR6) and serotonin 7 receptor (5-HTR7) in the brains of healthy or T. gondii -infected mice. Gene expression was detected by quantitative real-time PCR. β-Actin was used as a reference gene. The gene-specific primers are listed in the Material and Methods. The relative expression levels were calculated by the 2 (-ΔΔCT) method. Statistical analysis was performed using a one-way analysis of variance and Tukey's multiple comparison test. The values represent means ± S.D. ***p

    Article Snippet: 2.6 Relative quantification of gene expression Relative quantification analyses to determine the expression of 5-HTR2A, 5-HTR2C, 5-HTR6, 5-HTR7, and interleukin-6 (IL-6) mRNA levels were performed with StepOne Plus Real-Time PCR System (Applied Biosystem) using cDNA synthesized from HepG2 RNAs.

    Techniques: Expressing, Infection, Mouse Assay, Real-time Polymerase Chain Reaction

    Analysis of NIPSNAP1 mRNA expression induced by PGE 2 . (a) RT-PCR and real-time PCR analysis of NIPSNAP1 expression induced by 5 µM PGE 2 in DRG cells. (b) RT-PCR analysis of the expression of mRNA encoding EP subtypes in DRG cells. White arrowhead shows EP3β. (c) Effect of EP agonists on the expression of NIPSNAP1 mRNA. DRG cells were incubated for 1 h in the presence of each EP agonist (1 µM), and subjected to RT-PCR and real-time PCR analysis. (d) Effect of the protein kinase A inhibitor H-89 on the PGE 2 -induced expression of NIPSNAP1 mRNA. DRG cells incubated with 5 µM PGE 2 for 1 h in the absence and presence of 20 µM H-89 were subjected to RT-PCR and real-time PCR analysis. The upper and lower panels show representative results of RT-PCR and real-time PCR analysis, respectively. Data are expressed as the mean ± SEM ( n = 3–4). **p

    Journal: Molecular Pain

    Article Title: Involvement of NIPSNAP1, a neuropeptide nocistatin-interacting protein, in inflammatory pain

    doi: 10.1177/1744806916637699

    Figure Lengend Snippet: Analysis of NIPSNAP1 mRNA expression induced by PGE 2 . (a) RT-PCR and real-time PCR analysis of NIPSNAP1 expression induced by 5 µM PGE 2 in DRG cells. (b) RT-PCR analysis of the expression of mRNA encoding EP subtypes in DRG cells. White arrowhead shows EP3β. (c) Effect of EP agonists on the expression of NIPSNAP1 mRNA. DRG cells were incubated for 1 h in the presence of each EP agonist (1 µM), and subjected to RT-PCR and real-time PCR analysis. (d) Effect of the protein kinase A inhibitor H-89 on the PGE 2 -induced expression of NIPSNAP1 mRNA. DRG cells incubated with 5 µM PGE 2 for 1 h in the absence and presence of 20 µM H-89 were subjected to RT-PCR and real-time PCR analysis. The upper and lower panels show representative results of RT-PCR and real-time PCR analysis, respectively. Data are expressed as the mean ± SEM ( n = 3–4). **p

    Article Snippet: Reverse-transcription polymerase chain reaction (RT-PCR) amplifications of NIPSNAP1 and EPs were performed as follows: 1 cycle at 94℃ for 1 min followed by 10 cycles at 94℃ for 1 min and at 72℃ for 3 min, 15 cycles at 94℃ for 1 min, 65℃ for 2 min, and at 72℃ for 30 s, and 10 cycles at 94℃ for 1 min, 62℃ for 2 min, and at 72℃ for 30 s, and 1 cycle at 72℃ for 2 min. RT-PCR amplification of GAPDH was performed as follows: 1 cycle at 94℃ for 1 min followed by 35 cycles at 94℃ for 1 min, 60℃ for 1.5 min, and at 72℃ for 30 s, and finally 1 cycle at 72℃ for 7 min. mRNA levels were measured using quantitative real-time PCR with a StepOne System (Applied Biosystem) and GoTaq qPCR master mix (Promega).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Incubation

    Analysis of NIPSNAP1 mRNA levels following the induction of inflammation. Levels of NIPSNAP1 mRNA in DRG and spinal cord induced by injection into the dorsal surface of hind paw of 2% formalin (a) or 1% carrageenan (n). The upper and lower panels show representative results of RT-PCR and real-time PCR analysis, respectively. Data are expressed as the mean ± SEM ( n = 3). **p

    Journal: Molecular Pain

    Article Title: Involvement of NIPSNAP1, a neuropeptide nocistatin-interacting protein, in inflammatory pain

    doi: 10.1177/1744806916637699

    Figure Lengend Snippet: Analysis of NIPSNAP1 mRNA levels following the induction of inflammation. Levels of NIPSNAP1 mRNA in DRG and spinal cord induced by injection into the dorsal surface of hind paw of 2% formalin (a) or 1% carrageenan (n). The upper and lower panels show representative results of RT-PCR and real-time PCR analysis, respectively. Data are expressed as the mean ± SEM ( n = 3). **p

    Article Snippet: Reverse-transcription polymerase chain reaction (RT-PCR) amplifications of NIPSNAP1 and EPs were performed as follows: 1 cycle at 94℃ for 1 min followed by 10 cycles at 94℃ for 1 min and at 72℃ for 3 min, 15 cycles at 94℃ for 1 min, 65℃ for 2 min, and at 72℃ for 30 s, and 10 cycles at 94℃ for 1 min, 62℃ for 2 min, and at 72℃ for 30 s, and 1 cycle at 72℃ for 2 min. RT-PCR amplification of GAPDH was performed as follows: 1 cycle at 94℃ for 1 min followed by 35 cycles at 94℃ for 1 min, 60℃ for 1.5 min, and at 72℃ for 30 s, and finally 1 cycle at 72℃ for 7 min. mRNA levels were measured using quantitative real-time PCR with a StepOne System (Applied Biosystem) and GoTaq qPCR master mix (Promega).

    Techniques: Injection, Reverse Transcription Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Distribution of NIPSNAP1 mRNA. (a) RT-PCR analysis of NIPSNAP1 mRNA expression in the spinal cord, paw, and DRG. GAPDH served as the control. (b) In situ hybridization analysis of NIPSNAP1 mRNA expression in the spinal cords and dorsal root ganglia of wild-type and NIPSNAP1 −/− mice.

    Journal: Molecular Pain

    Article Title: Involvement of NIPSNAP1, a neuropeptide nocistatin-interacting protein, in inflammatory pain

    doi: 10.1177/1744806916637699

    Figure Lengend Snippet: Distribution of NIPSNAP1 mRNA. (a) RT-PCR analysis of NIPSNAP1 mRNA expression in the spinal cord, paw, and DRG. GAPDH served as the control. (b) In situ hybridization analysis of NIPSNAP1 mRNA expression in the spinal cords and dorsal root ganglia of wild-type and NIPSNAP1 −/− mice.

    Article Snippet: Reverse-transcription polymerase chain reaction (RT-PCR) amplifications of NIPSNAP1 and EPs were performed as follows: 1 cycle at 94℃ for 1 min followed by 10 cycles at 94℃ for 1 min and at 72℃ for 3 min, 15 cycles at 94℃ for 1 min, 65℃ for 2 min, and at 72℃ for 30 s, and 10 cycles at 94℃ for 1 min, 62℃ for 2 min, and at 72℃ for 30 s, and 1 cycle at 72℃ for 2 min. RT-PCR amplification of GAPDH was performed as follows: 1 cycle at 94℃ for 1 min followed by 35 cycles at 94℃ for 1 min, 60℃ for 1.5 min, and at 72℃ for 30 s, and finally 1 cycle at 72℃ for 7 min. mRNA levels were measured using quantitative real-time PCR with a StepOne System (Applied Biosystem) and GoTaq qPCR master mix (Promega).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, In Situ Hybridization, Mouse Assay

    Validation of methylated targets in LNcaP and DU145 cells . A) DNA was extracted using the DNeasy kit and total of 1 μg from parental (total) LNCaP and DU145 cells was bisulfite modified using the EpiTect Bisulfite kit from Qiagen. MS-PCR was performed using Platinum Taq Polymerase (Invitrogen) and 200 ng of either genomic of bisulfite treated DNA was used. The samples were visualized using a 1% agarose gel and ethidium bromide. Both Sox1 and Bmx are methylated in the LNCaP and DU145 cell lines. B) Total RNA was isolated using TRIzol and qRT-PCR analysis was performed using a StepOne Real-time PCR machine with TaqMan Gene Expression Assay reagents and probes. Isolation of DNA and cDNA from non-invasive and invasive cells was carried out as previously described in materials and methods. Relative fold induction of mRNA was compared between non-invasive and invasive cells using the Delta-Delta CT method of quantitation where the parental lines were set at 1.0 as the control, and 18S rRNA was used as a loading control. Increased levels of both Sox1 and Bmx are seen in invasive LNCaP and DU145 cells compared to the non-invasive and parental lines. Normal human prostate RNA was used as a control. A Two-way ANOVA with a Bonferroni post-test was performed to compare groups and * represents a p-value of

    Journal: Molecular Cancer

    Article Title: Epigenetic regulation of CpG promoter methylation in invasive prostate cancer cells

    doi: 10.1186/1476-4598-9-267

    Figure Lengend Snippet: Validation of methylated targets in LNcaP and DU145 cells . A) DNA was extracted using the DNeasy kit and total of 1 μg from parental (total) LNCaP and DU145 cells was bisulfite modified using the EpiTect Bisulfite kit from Qiagen. MS-PCR was performed using Platinum Taq Polymerase (Invitrogen) and 200 ng of either genomic of bisulfite treated DNA was used. The samples were visualized using a 1% agarose gel and ethidium bromide. Both Sox1 and Bmx are methylated in the LNCaP and DU145 cell lines. B) Total RNA was isolated using TRIzol and qRT-PCR analysis was performed using a StepOne Real-time PCR machine with TaqMan Gene Expression Assay reagents and probes. Isolation of DNA and cDNA from non-invasive and invasive cells was carried out as previously described in materials and methods. Relative fold induction of mRNA was compared between non-invasive and invasive cells using the Delta-Delta CT method of quantitation where the parental lines were set at 1.0 as the control, and 18S rRNA was used as a loading control. Increased levels of both Sox1 and Bmx are seen in invasive LNCaP and DU145 cells compared to the non-invasive and parental lines. Normal human prostate RNA was used as a control. A Two-way ANOVA with a Bonferroni post-test was performed to compare groups and * represents a p-value of

    Article Snippet: Quantitative real time polymerase chain reaction (qRT-PCR) analysis was performed using a StepOne Real-time PCR machine (Applied Biosystems, Foster City, CA) with TaqMan Gene Expression Assay reagents and probes (Applied Biosystems).

    Techniques: Methylation, Modification, Mass Spectrometry, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Isolation, Quantitative RT-PCR, Real-time Polymerase Chain Reaction, Expressing, Quantitation Assay

    MYB96 and HDA15 co-bind to the ROP promoters. In a , b , putative MYB-binding sites are indicated by arrowheads. Black underbars indicate the regions of PCR amplification after chromatin immunoprecipitation (ChIP). ChIP-quantitative PCR assays were conducted to examine enrichment of MYB96 and HDA15 at ROP loci. Three independent biological replicates were averaged, and statistical significance of the measurements was analyzed by Student’s t test (* P

    Journal: Nature Communications

    Article Title: MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis

    doi: 10.1038/s41467-019-09417-1

    Figure Lengend Snippet: MYB96 and HDA15 co-bind to the ROP promoters. In a , b , putative MYB-binding sites are indicated by arrowheads. Black underbars indicate the regions of PCR amplification after chromatin immunoprecipitation (ChIP). ChIP-quantitative PCR assays were conducted to examine enrichment of MYB96 and HDA15 at ROP loci. Three independent biological replicates were averaged, and statistical significance of the measurements was analyzed by Student’s t test (* P

    Article Snippet: RT-qPCR experiments were performed on the Step-One Plus Real-Time PCR System (Applied Biosystems).

    Techniques: Binding Assay, Polymerase Chain Reaction, Amplification, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    HDA15 and MYB96 co-regulate histone deacetylation at ROP loci. a Effects of abscisic acid (ABA) on H3ac accumulation at the ROP promoters in myb96-1 , hda15-1 , and myb96-1hda15-1 mutants. b Effects of ABA on H4ac accumulation at the ROP promoters. In a , b , 2-week-old seedlings grown under long days (LDs) were transferred to MS-liquid medium supplemented with 20 μM ABA and incubated for 24 h. Chromatin immunoprecipitation (ChIP) assays using anti-H3ac and anti-H4ac antibodies were performed. The indicated genomic regions (see Fig. 5 ) were analyzed by ChIP-quantitative PCR. Three independent biological replicates were averaged, and statistical significance of the measurements was analyzed by analysis of variance (ANOVA) (one-way ANOVA with Fisher’s post hoc test, * P

    Journal: Nature Communications

    Article Title: MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis

    doi: 10.1038/s41467-019-09417-1

    Figure Lengend Snippet: HDA15 and MYB96 co-regulate histone deacetylation at ROP loci. a Effects of abscisic acid (ABA) on H3ac accumulation at the ROP promoters in myb96-1 , hda15-1 , and myb96-1hda15-1 mutants. b Effects of ABA on H4ac accumulation at the ROP promoters. In a , b , 2-week-old seedlings grown under long days (LDs) were transferred to MS-liquid medium supplemented with 20 μM ABA and incubated for 24 h. Chromatin immunoprecipitation (ChIP) assays using anti-H3ac and anti-H4ac antibodies were performed. The indicated genomic regions (see Fig. 5 ) were analyzed by ChIP-quantitative PCR. Three independent biological replicates were averaged, and statistical significance of the measurements was analyzed by analysis of variance (ANOVA) (one-way ANOVA with Fisher’s post hoc test, * P

    Article Snippet: RT-qPCR experiments were performed on the Step-One Plus Real-Time PCR System (Applied Biosystems).

    Techniques: Mass Spectrometry, Incubation, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    Effects of proteasome inhibition on autophagy A. PIs induce autophagosome formation. LNCaP-Pro5 cells were treated with 100nM bortezomib (BZ) or NPI-0052 (NPI) for 24h. The black arrows identify autophagosome structures and the open arrows identify the early-aggresome like structures. B. PIs stimulate ATG gene expression. LNCaP-Pro5 cells were treated as above for indicated times and the expression of ATG5/7 was measured by one step-quantitative RT-PCR using the StepOne™ Real-time PCR systems. RQ, relative quantity; PPIA, cyclophilin A. C. Proteasome inhibition stimulates ATG gene expression. LNCaP-Pro5 cells were transfected with siRNA constructs specific for proteasome subunits β1, 2 5 or a non-targeted control siRNA for 72h. One step-quantitative RT-PCR for ATG5/7 was performed. Levels of the proteasome subunits were examined by immunoblotting and actin served as a loading control. Ctrl, Control; NS, Non-targeted control siRNA.

    Journal: Oncogene

    Article Title: Proteasome inhibitors activate autophagy as a cytoprotective response in human prostate cancer cells

    doi: 10.1038/onc.2009.343

    Figure Lengend Snippet: Effects of proteasome inhibition on autophagy A. PIs induce autophagosome formation. LNCaP-Pro5 cells were treated with 100nM bortezomib (BZ) or NPI-0052 (NPI) for 24h. The black arrows identify autophagosome structures and the open arrows identify the early-aggresome like structures. B. PIs stimulate ATG gene expression. LNCaP-Pro5 cells were treated as above for indicated times and the expression of ATG5/7 was measured by one step-quantitative RT-PCR using the StepOne™ Real-time PCR systems. RQ, relative quantity; PPIA, cyclophilin A. C. Proteasome inhibition stimulates ATG gene expression. LNCaP-Pro5 cells were transfected with siRNA constructs specific for proteasome subunits β1, 2 5 or a non-targeted control siRNA for 72h. One step-quantitative RT-PCR for ATG5/7 was performed. Levels of the proteasome subunits were examined by immunoblotting and actin served as a loading control. Ctrl, Control; NS, Non-targeted control siRNA.

    Article Snippet: One-step real-time RT-PCR was performed in triplicate using the AgPath-ID One-Step RT-PCR Kit (Ambion, Austin, TX) and the expression of each target gene was quantified using the StepOne™ Real-time PCR systems (Applied Biosystems, Foster City, CA).

    Techniques: Inhibition, Expressing, Quantitative RT-PCR, Real-time Polymerase Chain Reaction, Transfection, Construct

    Melting temperature analysis of eGFP, DHFR Mp and their chimera. ( A ) DHFR Mp , eGFP and a chimera of these proteins were subjected to temperature denaturation in bulk solution using a Real-Time PCR machine. Denaturation was monitored by measuring the change in fluorescence of the SYPRO Orange reagent. Each trace represents the average of at least six experiments. ( B ) Plots of the first derivatives of the denaturation curves as a function of temperature. Melting points were determined from these plots by using the StepOne Software v2.3. Temperature melts of eGFP, DHFR Mp and their chimera.

    Journal: eLife

    Article Title: Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization

    doi: 10.7554/eLife.56511

    Figure Lengend Snippet: Melting temperature analysis of eGFP, DHFR Mp and their chimera. ( A ) DHFR Mp , eGFP and a chimera of these proteins were subjected to temperature denaturation in bulk solution using a Real-Time PCR machine. Denaturation was monitored by measuring the change in fluorescence of the SYPRO Orange reagent. Each trace represents the average of at least six experiments. ( B ) Plots of the first derivatives of the denaturation curves as a function of temperature. Melting points were determined from these plots by using the StepOne Software v2.3. Temperature melts of eGFP, DHFR Mp and their chimera.

    Article Snippet: Measurements of melting temperatures of eGFP and DHFRMp The melting temperatures of eGFP and DHFRMp alone and in the chimera were measured by differential scanning fluorimetry using a StepOne real-time PCR instrument (Applied Biosystems).

    Techniques: Real-time Polymerase Chain Reaction, Fluorescence, Software

    The melting temperature of DHFR Mp increases in the presence of its substrates. ( A ) The chimera (5 µM) alone or in the presence of 500 µM NADPH or DHF was subjected to temperature denaturation using a Real-Time PCR machine as described under Materials and methods. Each trace represents the average of at least six experiments. ( B ) Plots of the first derivatives of the denaturation curves as a function of temperature. Melting points were determined from these plots by using the StepOne Software v2.3. Under the conditions here, the melting temperature of the DHFR Mp part of the chimera increases, in the presence of NADPH and DHF, by about 8°C and 31°C, respectively. Temperature melts of the chimera in the absence and presence of DHF or NADPH.

    Journal: eLife

    Article Title: Measuring protein stability in the GroEL chaperonin cage reveals massive destabilization

    doi: 10.7554/eLife.56511

    Figure Lengend Snippet: The melting temperature of DHFR Mp increases in the presence of its substrates. ( A ) The chimera (5 µM) alone or in the presence of 500 µM NADPH or DHF was subjected to temperature denaturation using a Real-Time PCR machine as described under Materials and methods. Each trace represents the average of at least six experiments. ( B ) Plots of the first derivatives of the denaturation curves as a function of temperature. Melting points were determined from these plots by using the StepOne Software v2.3. Under the conditions here, the melting temperature of the DHFR Mp part of the chimera increases, in the presence of NADPH and DHF, by about 8°C and 31°C, respectively. Temperature melts of the chimera in the absence and presence of DHF or NADPH.

    Article Snippet: Measurements of melting temperatures of eGFP and DHFRMp The melting temperatures of eGFP and DHFRMp alone and in the chimera were measured by differential scanning fluorimetry using a StepOne real-time PCR instrument (Applied Biosystems).

    Techniques: Real-time Polymerase Chain Reaction, Software

    Effects of OJS on miR-10a and miR-126 3p expression in the aorta of ApoE −/− mice. mRNA expression of adhesion molecules determined by real-time Reverse Transcription-PCR (RT-qPCR) analysis ( A ). Levels of miRNA determined by real-time RT-qPCR ( B ). Data are presented as means ± S.E. ** p

    Journal: Nutrients

    Article Title: The Inhibitory Effect of Ojeoksan on Early and Advanced Atherosclerosis

    doi: 10.3390/nu10091256

    Figure Lengend Snippet: Effects of OJS on miR-10a and miR-126 3p expression in the aorta of ApoE −/− mice. mRNA expression of adhesion molecules determined by real-time Reverse Transcription-PCR (RT-qPCR) analysis ( A ). Levels of miRNA determined by real-time RT-qPCR ( B ). Data are presented as means ± S.E. ** p

    Article Snippet: The real-time RT-qPCR was carried out with an SYBR Green PCR Master Mix (Enzynomics, Inc., Daejeon, Korea) and performed at an initial denaturation step at 95 °C for 10 min, followed by 40 cycles at 95 °C for 15 s, and finally 60 °C for 60 s in the Step-One™ Real-Time PCR System (Applied Biosystems, Foster City, CA, USA). miR-10a and miR-126 3p were measured by using a hsa-mir-10a Real-Time RT-PCR detection kit (CPK1014) and a hsa-mir-126 3p Real-Time RT-PCR detection kit (CPK1083) (Cohesion Biosciences., London, UK).

    Techniques: Expressing, Mouse Assay, Polymerase Chain Reaction, Quantitative RT-PCR

    Activating Endogenous Genes with TALEs HepG2 and PANC1 cells were transfected with HNF4α/E47-TALE1-VPR. (A) Expression of HNF4α and characteristic hepatocyte markers in HepG2 cells. (B) Expression of “stemness” genes in HepG2 cells. (C) Expression of E47, cell cycle arrest-related genes (p21 and TP53INP1), and E47 target genes (HNF6, SOX9, CX32, and MIST1) in PANC1 cells. Data analysis was performed with the Applied Biosystems StepOne software v2.3, and C t values of detected genes were normalized with that of β-actin. The relative expression level of target mRNAs was calculated as relative quantity (RQ) according to the equation: RQ = 2 −ΔΔCt . Student’s t test was used to check statistical significance. *p

    Journal: Molecular Therapy. Methods & Clinical Development

    Article Title: Generate TALE/TALEN as Easily and Rapidly as Generating CRISPR

    doi: 10.1016/j.omtm.2019.02.004

    Figure Lengend Snippet: Activating Endogenous Genes with TALEs HepG2 and PANC1 cells were transfected with HNF4α/E47-TALE1-VPR. (A) Expression of HNF4α and characteristic hepatocyte markers in HepG2 cells. (B) Expression of “stemness” genes in HepG2 cells. (C) Expression of E47, cell cycle arrest-related genes (p21 and TP53INP1), and E47 target genes (HNF6, SOX9, CX32, and MIST1) in PANC1 cells. Data analysis was performed with the Applied Biosystems StepOne software v2.3, and C t values of detected genes were normalized with that of β-actin. The relative expression level of target mRNAs was calculated as relative quantity (RQ) according to the equation: RQ = 2 −ΔΔCt . Student’s t test was used to check statistical significance. *p

    Article Snippet: The qPCR programs were run on a real-time PCR machine, StepOne Plus (Applied Biosystems).

    Techniques: Transfection, Expressing, Software

    Effect of fucoxanthin rich powder on mRNA expression of transcription factor and enzymes related to antioxidant system in the liver of rats. Total RNA was isolated using TRI-reagenet, and cDNA was synthesized using 3 ug of total RNA with SuperScript II reverse transcriptase. Realtime PCR was performed using SYBR green and standard procedures to assess the mRNA expression of the primer in liver samples obtained from each group. An Applied Biosystem StepOne softwere v2.1 was used. Each bar represents the mean ± S.E of three independent experiments. Different letters above each bar indicate significant differences among the groups at α = 0.05 as determined by Duncan's multiple range tests. HO-1: heme oxygenase (decycling) 1, Nrf2: nuclear factor, erythroid derived 2, like 2, NQO-1: NAD(P)H quinone oxidoreductase 1.

    Journal: Nutrition Research and Practice

    Article Title: Antioxidant effects of fucoxanthin rich powder in rats fed with high fat diet

    doi: 10.4162/nrp.2013.7.6.475

    Figure Lengend Snippet: Effect of fucoxanthin rich powder on mRNA expression of transcription factor and enzymes related to antioxidant system in the liver of rats. Total RNA was isolated using TRI-reagenet, and cDNA was synthesized using 3 ug of total RNA with SuperScript II reverse transcriptase. Realtime PCR was performed using SYBR green and standard procedures to assess the mRNA expression of the primer in liver samples obtained from each group. An Applied Biosystem StepOne softwere v2.1 was used. Each bar represents the mean ± S.E of three independent experiments. Different letters above each bar indicate significant differences among the groups at α = 0.05 as determined by Duncan's multiple range tests. HO-1: heme oxygenase (decycling) 1, Nrf2: nuclear factor, erythroid derived 2, like 2, NQO-1: NAD(P)H quinone oxidoreductase 1.

    Article Snippet: Ct-values of target genes and the reference gene were obtained using an Applied Biosystems StepOne Plus RT-PCR system (Applied biosystems, CA, USA).

    Techniques: Expressing, Isolation, Synthesized, Polymerase Chain Reaction, SYBR Green Assay, Derivative Assay

    Real time-PCR for GSK3-β; Total RNA was extracted; the standard reverse transcription was performed using RevertAid First Strand cDNA Synthesis Kit. Subsequent real time PCR was done with Power SYBR Green real time master mix and Stepone real time PCR (Applied Biosystems, Carlsbad, U.S.A.). GAPDH primer was used as a housekeeping gene. Each reaction was performed in triplicate. Expression of GSK3-β was down-regulated in non-obstructive azoospermia (3.10±0.19) compared with normal (7.12±0.39) and obstructive azoospermia (6.32±0.42) groups. The difference was significant (p=0.001)

    Journal: Iranian Journal of Reproductive Medicine

    Article Title: Expression of Glycogen synthase kinase 3-? (GSK3-?) gene in azoospermic men

    doi:

    Figure Lengend Snippet: Real time-PCR for GSK3-β; Total RNA was extracted; the standard reverse transcription was performed using RevertAid First Strand cDNA Synthesis Kit. Subsequent real time PCR was done with Power SYBR Green real time master mix and Stepone real time PCR (Applied Biosystems, Carlsbad, U.S.A.). GAPDH primer was used as a housekeeping gene. Each reaction was performed in triplicate. Expression of GSK3-β was down-regulated in non-obstructive azoospermia (3.10±0.19) compared with normal (7.12±0.39) and obstructive azoospermia (6.32±0.42) groups. The difference was significant (p=0.001)

    Article Snippet: Subsequent real time PCR was done with Power Syber Green real time master mix and Stepone real time PCR (Applied biosystems, Carlsbad, USA).

    Techniques: Real-time Polymerase Chain Reaction, SYBR Green Assay, Expressing

    Amplification plot obtained by the StepOne system software using Method II. ND: non-digested sample; Hpa II: sample digested with Hpa II, a methylation-sensitive restriction enzyme; Msp I: sample digested with Msp I, an isoschizomer of Hpa II, which is insensitive to methylation; t: threshold.

    Journal: Brazilian Journal of Medical and Biological Research

    Article Title: Placental hydroxymethylation vsmethylation at the imprinting control region 2 on chromosome 11p15.5

    doi: 10.1590/1414-431X20133035

    Figure Lengend Snippet: Amplification plot obtained by the StepOne system software using Method II. ND: non-digested sample; Hpa II: sample digested with Hpa II, a methylation-sensitive restriction enzyme; Msp I: sample digested with Msp I, an isoschizomer of Hpa II, which is insensitive to methylation; t: threshold.

    Article Snippet: The digested material obtained by both methods was analyzed by real-time PCR [comparative Ct method ( )] ( ) using the StepOne system (Applied Biosystems, USA), and the results were normalized by the formula (1/2)a−b , where “a” corresponds to the Ct value resulting from treatments numbered from one to six of Method I (individually), and “b” corresponds to the Ct value from Treatment number 6 ( ) ( ).

    Techniques: Amplification, Software, Methylation

    Correlations between cytokine mRNA expression (derived from Realtime-PCR) and ruminal factors. a - c : Correlation analysis between IL-1 , IL-2 , IL-6 relative mRNA expressions and ruminal pH. d - f : Correlation analysis between IL-1 , IL-2 , IL-6 relative mRNA expressions and ruminal LPS

    Journal: Journal of Animal Science and Biotechnology

    Article Title: High-concentrate feeding upregulates the expression of inflammation-related genes in the ruminal epithelium of dairy cattle

    doi: 10.1186/s40104-016-0100-1

    Figure Lengend Snippet: Correlations between cytokine mRNA expression (derived from Realtime-PCR) and ruminal factors. a - c : Correlation analysis between IL-1 , IL-2 , IL-6 relative mRNA expressions and ruminal pH. d - f : Correlation analysis between IL-1 , IL-2 , IL-6 relative mRNA expressions and ruminal LPS

    Article Snippet: Reactions were run in a StepOne Plus Realtime PCR System (Applied Biosystems).

    Techniques: Expressing, Derivative Assay, Polymerase Chain Reaction