reverse transcription quantitative pcr rt qpcr Search Results


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  • 99
    Thermo Fisher high capacity cdna reverse transcription kit
    HIV-1 Tg26 transgenic mice express viral mRNA in neurogenic regions. a Diagram of the truncated HIV-1 NL4-3 proviral genome in HIV-1 Tg26 mice, showing a deletion of 3.1 kb DNA spanning a majority of the Gag and Pol genes, and the predicted presence of seven viral gene transcripts. b RT-qPCR analysis of viral gene transcripts in neurogenic regions of HIV-1 Tg26 mice. Equal amount of <t>RNA</t> from the SVZs, SGZs, olfactory bulbs (OB), and kidneys of HIV-1 Tg26 mice was reverse transcribed, with 2 ng of the generated <t>cDNA</t> used for real-time PCR with primers covering p17 gag , tat 1 (unspliced variant), tat 2 (spliced variant), env ( gp120 ), vpu , and nef . Samples were collected from four HIV-1 Tg26 mice (two males and two females), and reactions were run in triplicate. Values are expressed as mean ± SEM
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    Bio-Rad rt qpcr
    HIV-1 Tg26 transgenic mice express viral mRNA in neurogenic regions. a Diagram of the truncated HIV-1 NL4-3 proviral genome in HIV-1 Tg26 mice, showing a deletion of 3.1 kb DNA spanning a majority of the Gag and Pol genes, and the predicted presence of seven viral gene transcripts. b RT-qPCR analysis of viral gene transcripts in neurogenic regions of HIV-1 Tg26 mice. Equal amount of <t>RNA</t> from the SVZs, SGZs, olfactory bulbs (OB), and kidneys of HIV-1 Tg26 mice was reverse transcribed, with 2 ng of the generated <t>cDNA</t> used for real-time PCR with primers covering p17 gag , tat 1 (unspliced variant), tat 2 (spliced variant), env ( gp120 ), vpu , and nef . Samples were collected from four HIV-1 Tg26 mice (two males and two females), and reactions were run in triplicate. Values are expressed as mean ± SEM
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    Bio-Rad quantitative reverse transcription polymerase chain reaction
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher rt qpcr
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher thermoscript rt pcr system
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher rt pcr
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher taqman microrna reverse transcription kit
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Qiagen quantitect reverse transcription kit
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher total rna
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    TaKaRa primescript rt reagent kit
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Bio-Rad rt pcr
    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and <t>quantitative</t> <t>reverse</t> <t>transcription</t> <t>polymerase</t> <t>chain</t> <t>reaction</t> (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P
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    Thermo Fisher superscript iii first strand synthesis supermix for qrt pcr
    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
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    Qiagen quantitect sybr green rt pcr kit
    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
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    Thermo Fisher taqpath 1 step rt qpcr master mix
    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
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    Bio-Rad quantitative real time rt pcr
    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
    Quantitative Real Time Rt Pcr, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 92/100, based on 289 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
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    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by <t>qRT-PCR</t> 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) <t>Three-color</t> multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P
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    Image Search Results


    HIV-1 Tg26 transgenic mice express viral mRNA in neurogenic regions. a Diagram of the truncated HIV-1 NL4-3 proviral genome in HIV-1 Tg26 mice, showing a deletion of 3.1 kb DNA spanning a majority of the Gag and Pol genes, and the predicted presence of seven viral gene transcripts. b RT-qPCR analysis of viral gene transcripts in neurogenic regions of HIV-1 Tg26 mice. Equal amount of RNA from the SVZs, SGZs, olfactory bulbs (OB), and kidneys of HIV-1 Tg26 mice was reverse transcribed, with 2 ng of the generated cDNA used for real-time PCR with primers covering p17 gag , tat 1 (unspliced variant), tat 2 (spliced variant), env ( gp120 ), vpu , and nef . Samples were collected from four HIV-1 Tg26 mice (two males and two females), and reactions were run in triplicate. Values are expressed as mean ± SEM

    Journal: Journal of Neuroinflammation

    Article Title: Adult neurogenic deficits in HIV-1 Tg26 transgenic mice

    doi: 10.1186/s12974-018-1322-2

    Figure Lengend Snippet: HIV-1 Tg26 transgenic mice express viral mRNA in neurogenic regions. a Diagram of the truncated HIV-1 NL4-3 proviral genome in HIV-1 Tg26 mice, showing a deletion of 3.1 kb DNA spanning a majority of the Gag and Pol genes, and the predicted presence of seven viral gene transcripts. b RT-qPCR analysis of viral gene transcripts in neurogenic regions of HIV-1 Tg26 mice. Equal amount of RNA from the SVZs, SGZs, olfactory bulbs (OB), and kidneys of HIV-1 Tg26 mice was reverse transcribed, with 2 ng of the generated cDNA used for real-time PCR with primers covering p17 gag , tat 1 (unspliced variant), tat 2 (spliced variant), env ( gp120 ), vpu , and nef . Samples were collected from four HIV-1 Tg26 mice (two males and two females), and reactions were run in triplicate. Values are expressed as mean ± SEM

    Article Snippet: Equal amounts (100 ng) of RNA from each sample was used for reverse transcription with the High Capacity cDNA Reverse Transcription Kit (Thermo Fischer Scientific Cat.# 4368814), and 2 ng of cDNA was applied for qPCR using specific primers (Table , Fig. a) targeting partial gag ( p17 ), tat (spliced and unspliced variants), env ( gp120 ), vpu , and nef based on previously published reports [ , ].

    Techniques: Transgenic Assay, Mouse Assay, Quantitative RT-PCR, Generated, Real-time Polymerase Chain Reaction, Variant Assay

    Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P

    Journal: Reproductive Sciences

    Article Title: A Preliminary Study: Human Fibroid Stro-1+/CD44+ Stem Cells Isolated From Uterine Fibroids Demonstrate Decreased DNA Repair and Genomic Integrity Compared to Adjacent Myometrial Stro-1+/CD44+Cells

    doi: 10.1177/1933719118783252

    Figure Lengend Snippet: Fibroid (F) stem cells differentially express DNA double-strand break repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation of genes relating to DNA double-strand break (DSB) repair, specifically nonhomologous end-joining (NHEJ) and other DSB repair–related genes (FC, P value). A, NHEJ: XRCC4 (0.26, P = .40) and XRCC6 (−0.42, P = .10). B, Other DNA DSB repair–related genes: RB1 (0.16, P = .25), SUMO1 (−0.65, P = .02), and XRCC2 (−1.3, P = .03). Bars represent log2 fold change expression from PrimePCR (black bars) or qRT-PCR validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, 1-sample t test. * P

    Article Snippet: Gene expression analysis by quantitative reverse transcription polymerase chain reaction To verify the results obtained by the DNA Damage PrimePCR array , quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR; Bio-Rad CFX96) was performed in n = 5 patient pairs (to confirm in the original 3 pairs + 3 additional patient pairs) of human F vs Myo stem cells for 5 and 22 genes shown to be consistently up- and downregulated, respectively, among the initial n = 3 patient pairs of F versus Myo stem cells.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Non-Homologous End Joining, Expressing, One-tailed Test

    Fibroid (F) stem cells differentially express homologous recombination (HR) DNA repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and qRT-PCR validation of genes relating to DNA double-strand break (DSB) repair, specifically HR, (FC, P value). A, DSB sensors : MRE11A (−0.91, P = .06), NBS1 (−0.97, P = .04), and RAD50 (−1.3, P = .01). B, HR DSB binding: BRCA2 (−1.7, P = .004), RAD51 (−1.3; P = .01), RAD51AP1 (−0.9, P = .12), and RAD52 (−1.1; P = .03). C, Cell cycle checkpoint control/arrest: RAD1 (−0.8, P = .06), RAD9A (−0.98; P = .03), and RAD17 (−0.55; P = .0.6). D, HR mediators and effectors: BARD1 (−1.3; P = .03), BRCA1 (−1.8; P = .01), MDC1 (−2.8; P = .06), CHEK1 (−1.2, P = .001), and CHEK2 (−0.9; P = .02). E, p53 signal transduction: CDKN1A (0.18, P = .19), MDM2 (1.2, P = .10), TP53 (−1.1, P = .009), and TP53BP1 (−0.96, P = .03). F, DNA DSB signal transduction: ataxia telangiectasia-mutated ( ATM ; −1, P = .04) and Ataxia Telangiectasia and Rad3-related protein ( ATR ;0.23, P = .002). Bars represent log2 fold change expression from PrimePCR (black bars) or quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, one-sample t test. * P

    Journal: Reproductive Sciences

    Article Title: A Preliminary Study: Human Fibroid Stro-1+/CD44+ Stem Cells Isolated From Uterine Fibroids Demonstrate Decreased DNA Repair and Genomic Integrity Compared to Adjacent Myometrial Stro-1+/CD44+Cells

    doi: 10.1177/1933719118783252

    Figure Lengend Snippet: Fibroid (F) stem cells differentially express homologous recombination (HR) DNA repair-related genes versus adjacent myometrial (Myo) stem cells. PrimePCR and qRT-PCR validation of genes relating to DNA double-strand break (DSB) repair, specifically HR, (FC, P value). A, DSB sensors : MRE11A (−0.91, P = .06), NBS1 (−0.97, P = .04), and RAD50 (−1.3, P = .01). B, HR DSB binding: BRCA2 (−1.7, P = .004), RAD51 (−1.3; P = .01), RAD51AP1 (−0.9, P = .12), and RAD52 (−1.1; P = .03). C, Cell cycle checkpoint control/arrest: RAD1 (−0.8, P = .06), RAD9A (−0.98; P = .03), and RAD17 (−0.55; P = .0.6). D, HR mediators and effectors: BARD1 (−1.3; P = .03), BRCA1 (−1.8; P = .01), MDC1 (−2.8; P = .06), CHEK1 (−1.2, P = .001), and CHEK2 (−0.9; P = .02). E, p53 signal transduction: CDKN1A (0.18, P = .19), MDM2 (1.2, P = .10), TP53 (−1.1, P = .009), and TP53BP1 (−0.96, P = .03). F, DNA DSB signal transduction: ataxia telangiectasia-mutated ( ATM ; −1, P = .04) and Ataxia Telangiectasia and Rad3-related protein ( ATR ;0.23, P = .002). Bars represent log2 fold change expression from PrimePCR (black bars) or quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation (checkered bars) in F (relative to adjacent Myo control stem cells) ± standard error of the mean. Mean log2 fold change was compared to 0 using one-tailed, one-sample t test. * P

    Article Snippet: Gene expression analysis by quantitative reverse transcription polymerase chain reaction To verify the results obtained by the DNA Damage PrimePCR array , quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR; Bio-Rad CFX96) was performed in n = 5 patient pairs (to confirm in the original 3 pairs + 3 additional patient pairs) of human F vs Myo stem cells for 5 and 22 genes shown to be consistently up- and downregulated, respectively, among the initial n = 3 patient pairs of F versus Myo stem cells.

    Techniques: Homologous Recombination, Quantitative RT-PCR, Binding Assay, Transduction, Expressing, Reverse Transcription Polymerase Chain Reaction, One-tailed Test

    Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by qRT-PCR 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) Three-color multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P

    Journal: JCI Insight

    Article Title: Liver epithelial focal adhesion kinase modulates fibrogenesis and hedgehog signaling

    doi: 10.1172/jci.insight.141217

    Figure Lengend Snippet: Hh/Smo pathway gene expression was determined in FAK-deficient hepatocytes and fibrotic hepatocyte-specific FAK-deficient liver. ( A ) Isolated hepatocytes from 6- to 8-week-old FAK fl/fl Alb-Cre – (WT) and FAK fl/fl Alb-Cre + (FAK –/– ) mice on normal chow diet were cultured on collagen-coated polyacr ylamide gels of 140 Pa, 1 kPa, or 6 kPa stiffness. Ihh mRNA expression was determined by qRT-PCR 24 hours later. Sample size n = 5–6 per group. ( B ) Stellate cells were isolated from WT and FAK –/– mice with DDC-induced fibrosis. Expression of Hh/Smo pathway genes and stellate cell activation markers was determined by qRT-PCR. Sample size n = 4 per group. ( C ) Three-color multiplexed RNAscope analysis of Smo , Adgre1 , and Krt19 was performed on DDC-induced fibrotic liver tissues of FAK fl/fl mice treated with AAV8-TBG-Null (Null) or AAV8-TBG-Cre (Cre). Images are representative of n = 4 per group. Scale bar: 20 μm. ( D ) Number of Smo + dots that were colocalized with Adgre1 + macrophages. ( E ) Number of Smo + dots that were colocalized with Krt19 + biliary cells. For D and E , 10 portal areas were analyzed per mouse, and at least 20 Adgre1 + or Krt19 + cells were analyzed per portal area; sample size was n = 4 per group. * P

    Article Snippet: Quantitative real-time reverse transcription PCR.

    Techniques: Expressing, Isolation, Mouse Assay, Cell Culture, Quantitative RT-PCR, Activation Assay