quantitative real-time pcr qpcr Search Results


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  • 99
    Thermo Fisher quantitative rt pcr qpcr
    Quantitative Rt Pcr Qpcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 495 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore real time quantitative pcr qpcr
    Ctt1 protein persists over time. Levels of CTT1 mRNA (dark blue line) and FLAG-tagged Ctt1 protein (light blue line) were measured throughout the experiment by quantitative <t>PCR</t> and Western analysis, respectively. Fold-change in FLAG-tagged CTT1 mRNA was
    Real Time Quantitative Pcr Qpcr, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher real time pcr qpcr
    Real-Time Quantitative <t>PCR</t> Analysis
    Real Time Pcr Qpcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2568 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kapa Biosystems quantitative real time pcr quantitative real time polymerase chain reaction qpcr
    Real-Time Quantitative <t>PCR</t> Analysis
    Quantitative Real Time Pcr Quantitative Real Time Polymerase Chain Reaction Qpcr, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eppendorf AG real time quantitative pcr qpcr
    H3K27me3 and LHP1 distribution on FLC. (A) Expression at various developmental stages in wild-type and lif2 plants. Semi-quantitative <t>RT-PCR</t> were performed on seven-day-old in vitro seedlings, rosette leaves after bolting (RL), floral buds just after bolting (FB1) and floral buds after the production of 10 siliques (FB2). The EF-1α gene expression was used as a control. (B) Schematic representation of the FLC locus and the 8 amplified regions used in chromatin immunoprecipitation (ChIP) assays. (C) ChIP analysis to determine the relative level of H3K27me3 at the indicated FLC regions in wild-type and lif2 seedlings. Immunoprecipitated DNA was analyzed by real-time <t>qPCR,</t> and enrichment was calculated as percentage of INPUT. All ChIP experiments were normalized for histone H3 occupancy and normed by using ChIP results on an AGAMOUS control region. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error. (D–F) Complementation of the lhp1 mutant by the expression of the genomic LHP1:MYC-tagged construct. (D) Plant phenotypes, (E) total number of rosette leaves, and (F) protein levels. (G) ChIP assays to determine the relative level of LHP1 binding at the indicated FLC regions in wild-type and lif2 backgrounds expressing the LHP1:MYC-tagged construct. A CONSTANS (CO) region was used as a negative control [23] . Immunoprecipitated DNA was analyzed by real-time qPCR, and enrichment was calculated as percentage of INPUT and normalized relative to a Col-0 control, represented as a dashed line. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error.
    Real Time Quantitative Pcr Qpcr, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad quantitative real time pcr quantitative real time pcr qpcr
    Co-occupancy of ZNF274, KAP1 and SETDB1 at a ZNF 3′ end in vivo. A) <t>ChIP-qPCR</t> confirmation of a set of ZNF274 targets. Quantitative real-time <t>PCR</t> (qPCR) for 10 target regions identified by ChIP-seq and three negative regions (GAPDH, CDH1, and ZNF44) was performed. The fold enrichment of each site was calculated as 2 to the power of the cycle threshold (cT) difference between input chromatin and ChIP samples. The results in the graph are the mean of three independent replicates with standard deviation. Primers used in these experiments can be found in Supplementary Table S5 . B) Sequential chromatin immunoprecipitation of ZNF274 and KAP1 in K562 cells. ZNF274 or KAP1 ChIP samples were sequentially immunoprecipitated using the indicated antibodies. The samples were analyzed by PCR and agarose gel electrophoresis with ethidium bromide staining using specific primer sets to ZNF180 , a zinc finger gene bound by ZNF274; ZNF555, a zinc finger gene not bound by ZNF274, but bound by KAP1; STX16 , and a non-zinc finger gene bound by neither ZNF274 nor KAP1.
    Quantitative Real Time Pcr Quantitative Real Time Pcr Qpcr, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 92/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eurofins quantitative real time pcr qpcr primers
    2.6. Quantitative <t>PCR</t> analysis of olfactory genes
    Quantitative Real Time Pcr Qpcr Primers, supplied by Eurofins, used in various techniques. Bioz Stars score: 95/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quantitative real time pcr qpcr trizol
    Polysome-profiling to identify ISG mRNAs subject to mTOR-dependent translational control. (A) RNA isolated from WISH cells treated with IFN β (100pM) in combination with DMSO or 1μM Torin1 for 12 hrs was subjected to comparative genome-wide mRNA expression profiling, and genes showing differential translation were identified using anota. Genes are plotted according to changes (Δ) in cytoplasmic and polysomal mRNA levels upon the addition of Torin1 to IFN β-treated cells. Genes showing repressed (blue) and enhanced (orange) mRNA translation in response to Torin1 are indicated. (B) Correlation between Torin1 (square)- and rapamycin (triangle)-induced mRNA translation changes (Δ) in IFN β-treated cells. Genes identified in either comparison that show increased (yellow) or decreased (blue) translation are indicated by condition where they were identified (squares or triangles). (C) A lack of correlation is observed when Torin1-induced mRNA translation changes (y-axis) and IFN β-induced cytoplasmic mRNA changes (x-axis) are plotted for all assessed genes. (D) NT5C3A mRNA variants 3 and 4 are transcriptionally induced by IFN. Schematic representation of NT5C3A mRNA variant-specific <t>PCR</t> primers used for <t>qPCR.</t> Arrows represent forward and reverse primers. mRNA abundance in nanograms (ng) was assessed by quantitative polymerase chain reaction (qPCR) for the indicated genes, including mRNA variants 1–4 of NT5C3A . Shown are means +/- standard deviations (n = 3). Theoretical transcriptional start sites (arrows) based on NCBI reference sequences are shown (box). (E) Cytoplasmic and polysomal mRNA abundance (ng) was assessed by qPCR for the indicated genes. Shown are means +/- standard deviations (n = 3). * indicates p-values
    Quantitative Real Time Pcr Qpcr Trizol, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad quantitative real time polymerase chain reaction qpcr quantitative real time pcr
    Polysome-profiling to identify ISG mRNAs subject to mTOR-dependent translational control. (A) RNA isolated from WISH cells treated with IFN β (100pM) in combination with DMSO or 1μM Torin1 for 12 hrs was subjected to comparative genome-wide mRNA expression profiling, and genes showing differential translation were identified using anota. Genes are plotted according to changes (Δ) in cytoplasmic and polysomal mRNA levels upon the addition of Torin1 to IFN β-treated cells. Genes showing repressed (blue) and enhanced (orange) mRNA translation in response to Torin1 are indicated. (B) Correlation between Torin1 (square)- and rapamycin (triangle)-induced mRNA translation changes (Δ) in IFN β-treated cells. Genes identified in either comparison that show increased (yellow) or decreased (blue) translation are indicated by condition where they were identified (squares or triangles). (C) A lack of correlation is observed when Torin1-induced mRNA translation changes (y-axis) and IFN β-induced cytoplasmic mRNA changes (x-axis) are plotted for all assessed genes. (D) NT5C3A mRNA variants 3 and 4 are transcriptionally induced by IFN. Schematic representation of NT5C3A mRNA variant-specific <t>PCR</t> primers used for <t>qPCR.</t> Arrows represent forward and reverse primers. mRNA abundance in nanograms (ng) was assessed by quantitative polymerase chain reaction (qPCR) for the indicated genes, including mRNA variants 1–4 of NT5C3A . Shown are means +/- standard deviations (n = 3). Theoretical transcriptional start sites (arrows) based on NCBI reference sequences are shown (box). (E) Cytoplasmic and polysomal mRNA abundance (ng) was assessed by qPCR for the indicated genes. Shown are means +/- standard deviations (n = 3). * indicates p-values
    Quantitative Real Time Polymerase Chain Reaction Qpcr Quantitative Real Time Pcr, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Stratagene real time pcr real time quantitative pcr qpcr
    p63 is significantly down-regulated in UM cell lines. ( A ) Representative western blot showing relative protein levels of endogenous p63 protein in UM cell lysates. Skin cell lysate served as a positive control for p63 antibody. ( B ) mRNA was extracted from non-transfected (NT) OCM-1 as well as from A431 cells and p63-tGFP-transfected OCM-1 cells used as positive controls for p63 expression. Quantitative <t>PCR</t> was performed to assess mRNA levels by analysing the amplification plots and dissociation curves for each of the three types of cells. NTC, non-template control.
    Real Time Pcr Real Time Quantitative Pcr Qpcr, supplied by Stratagene, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher real time quantitative pcr qpcr
    Thymic reconstitution is not dependent on the stem cell source employed or GvHD occurrence. Mean (±SE) number of log10 TREC was measured by quantitative <t>PCR,</t> before, and 3 and 6 months after transplantation in patients that received either a haploidentical hematopoietic Stem Cell Transplantation (Haplo, N = 33) or a Cord Blood Unrelated Donor Graft (CB, N = 24). Signal Joint (sj) TREC were quantified in ( A,C,E, and F ) and betaTREC in ( B and D ). Results were expressed by 150,000 Peripheral Blood Mononuclear Cells in ( A and B ) and by μL of blood in ( C,D,E, and F ). Patients were subsequently subdivided according to GvHD occurrence ( E and F ).
    Real Time Quantitative Pcr Qpcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2611 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Quanta Biosciences real time quantitative pcr qpcr
    UPR target gene activation precedes Tm-induced steatosis. (A–C) Larvae were treated starting on 3 dpf with DMSO and 0.25 μg/ml Tm and collected at the indicated time points. At least 15 larvae were stained with Oil Red O and scored for steatosis (A) and at least 5 livers were dissected for RNA extraction (B,C). (A) The log odds ratio of steatosis was plotted versus time (see Materials and Methods and supplementary material Table S3 ). (B) UPR target gene analysis measured by <t>qPCR</t> in liver cDNAs from the same cohorts assessed for steatosis in A. Expression of each gene is plotted as log fold change (log FC) over time (see Materials and Methods and supplementary material Table S7 ). (C) <t>PCR</t> analysis of xbp1 splicing with the percentage of spliced/total xbp1 for each sample plotted ( n =2). * P
    Real Time Quantitative Pcr Qpcr, supplied by Quanta Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche quantitative real time pcr qpcr quantitative real time pcr
    Part of the promoter sequence of UBC and the primer sequence of UBC_3 (depicted bold and underlined). The <t>qPCR</t> fragment is located around the transcription start site (CTG, italic underlined), starting from 31 bp upstream of the 5′-UTR (Untranslated Region) to 155 bp into this region and 553 bp upstream of the translation start codon (ATG, italic underlined). In the <t>PCR</t> fragment of the UBC_3 primers there are 14 CpG sites, of which one or more have differential methylation.
    Quantitative Real Time Pcr Qpcr Quantitative Real Time Pcr, supplied by Roche, 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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    TaKaRa quantitative real time pcr qpcr trizol
    Part of the promoter sequence of UBC and the primer sequence of UBC_3 (depicted bold and underlined). The <t>qPCR</t> fragment is located around the transcription start site (CTG, italic underlined), starting from 31 bp upstream of the 5′-UTR (Untranslated Region) to 155 bp into this region and 553 bp upstream of the translation start codon (ATG, italic underlined). In the <t>PCR</t> fragment of the UBC_3 primers there are 14 CpG sites, of which one or more have differential methylation.
    Quantitative Real Time Pcr Qpcr Trizol, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa quantitative real time pcr quantitative real time pcr qpcr
    Interleukin-4 (IL-4) and melatonin downregulated the expression of intercellular cell adhesion molecule-1 (ICAM-1) induced with D-glucose or interleukin-1β. After D-glucose (30 mM; 48 h incubation) or interleukin-1β (IL-1β; 10 ng/ml; 24 h incubation) induction with or without IL-4 (40 ng/ml) or melatonin (100 μM), total RNA was extracted from the human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells, and the supernatants were harvested for quantitative real-time <t>PCR</t> <t>(qPCR)</t> and enzyme-linked immunosorbent assay (ELISA) to measure the levels of ICAM-1 mRNA and protein, respectively. The mRNA and protein levels of ICAM-1 increased significantly after induction with D-glucose or IL-1β, but were significantly downregulated by IL-4 and melatonin. The data are expressed as the mean± standard deviation (SD; n = 4; *p
    Quantitative Real Time Pcr Quantitative Real Time Pcr Qpcr, supplied by TaKaRa, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies real time quantitative pcr qpcr
    <t>PCR</t> and <t>qPCR</t> validation of candidate transcripts. (A) PCR amplification (all 36 cycles) of candidate genes from different lines. PDS was used as a positive control. (B) Relative expression levels of green and purple B. juncea ( eEF1B α 2 was used as an internal control). (C) Relative gene expression levels under cold and high light treatment ( eEF1B α 2 was used as an internal control). ** Means statistically significant.
    Real Time Quantitative Pcr Qpcr, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 52 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa quantitative real time pcr qpcr kits
    <t>PCR</t> and <t>qPCR</t> validation of candidate transcripts. (A) PCR amplification (all 36 cycles) of candidate genes from different lines. PDS was used as a positive control. (B) Relative expression levels of green and purple B. juncea ( eEF1B α 2 was used as an internal control). (C) Relative gene expression levels under cold and high light treatment ( eEF1B α 2 was used as an internal control). ** Means statistically significant.
    Quantitative Real Time Pcr Qpcr Kits, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    PrimerDesign Inc quantitative real time pcr qpcr kit
    <t>PCR</t> and <t>qPCR</t> validation of candidate transcripts. (A) PCR amplification (all 36 cycles) of candidate genes from different lines. PDS was used as a positive control. (B) Relative expression levels of green and purple B. juncea ( eEF1B α 2 was used as an internal control). (C) Relative gene expression levels under cold and high light treatment ( eEF1B α 2 was used as an internal control). ** Means statistically significant.
    Quantitative Real Time Pcr Qpcr Kit, supplied by PrimerDesign Inc, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tiangen biotech co quantitative real time pcr quantitative real time pcr qpcr
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Quantitative Real Time Pcr Quantitative Real Time Pcr Qpcr, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa real time polymerase chain reaction qpcr real time pcr
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Real Time Polymerase Chain Reaction Qpcr Real Time Pcr, supplied by TaKaRa, used in various techniques. Bioz Stars score: 89/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher real time quantitative rt qpcr
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Real Time Quantitative Rt Qpcr, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BioTrove Inc real time quantitative pcr qpcr analysis
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Real Time Quantitative Pcr Qpcr Analysis, supplied by BioTrove Inc, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bioneer Corporation quantitative real time pcr quantitative real time pcr qpcr
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Quantitative Real Time Pcr Quantitative Real Time Pcr Qpcr, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quantitative real time pcr qpcr taqman assays
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
    Quantitative Real Time Pcr Qpcr Taqman Assays, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Meridian Life Science quantitative real time pcr qpcr quantitative real time pcr
    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
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    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
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    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
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    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
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    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by <t>RT-PCR</t> at 72 h post-infection. ( C ) <t>qPCR</t> results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p
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    (a) H E staining showing the junction between normal epithelium and severe dysplasia in human papillomavirus ( HPV )‐positive tonsil squa‐mous cell carcinoma (top left). Although some flattening of cells at the apical surface may exist, the majority of the abnormal epithelium has a poorly differentiated dense basaloid appearance with nuclear pleomorphism. MCM 7 (top right) and Ki67 (bottom left) staining are present in more than two‐thirds of the abnormal epithelium. In situ hybridization reveals an elevated level of HPV 16 DNA (bottom right) in the dysplastic epithelium when compared to the normal region (magnification, ×100; inset, ×150; Infinity capture software). ISH , in situ hybridization. (b) Reverse transcription–real‐time quantitative <t>PCR</t> ( RT ‐ <t>qPCR</t> ) analysis for all HPV ‐positive sample types showing significant differential expression of SYCP 2 (log2 fold change, 3.1 [95% confidence interval, 1.8–4.4]; P
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    Image Search Results


    Ctt1 protein persists over time. Levels of CTT1 mRNA (dark blue line) and FLAG-tagged Ctt1 protein (light blue line) were measured throughout the experiment by quantitative PCR and Western analysis, respectively. Fold-change in FLAG-tagged CTT1 mRNA was

    Journal: Genetics

    Article Title: Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae

    doi: 10.1534/genetics.112.143016

    Figure Lengend Snippet: Ctt1 protein persists over time. Levels of CTT1 mRNA (dark blue line) and FLAG-tagged Ctt1 protein (light blue line) were measured throughout the experiment by quantitative PCR and Western analysis, respectively. Fold-change in FLAG-tagged CTT1 mRNA was

    Article Snippet: Expression of selected genes was measured by real-time quantitative PCR (qPCR) using SYBR Green Jumpstart Taq (Sigma) and an Applied Biosystems 7500 detector (Foster City, CA).

    Techniques: Real-time Polymerase Chain Reaction, Western Blot

    The effect of NPC subunits on the faster expression response of TSA2 . The average log2 fold-change in TSA2 transcript was scored by quantitative PCR in wild-type, nup42Δ , nup59Δ , and nup100Δ cells as described in and in

    Journal: Genetics

    Article Title: Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae

    doi: 10.1534/genetics.112.143016

    Figure Lengend Snippet: The effect of NPC subunits on the faster expression response of TSA2 . The average log2 fold-change in TSA2 transcript was scored by quantitative PCR in wild-type, nup42Δ , nup59Δ , and nup100Δ cells as described in and in

    Article Snippet: Expression of selected genes was measured by real-time quantitative PCR (qPCR) using SYBR Green Jumpstart Taq (Sigma) and an Applied Biosystems 7500 detector (Foster City, CA).

    Techniques: Expressing, Real-time Polymerase Chain Reaction

    Real-Time Quantitative PCR Analysis

    Journal: Investigative Ophthalmology & Visual Science

    Article Title: RF/6A Chorioretinal Cells Do Not Display Key Endothelial Phenotypes

    doi: 10.1167/iovs.18-25215

    Figure Lengend Snippet: Real-Time Quantitative PCR Analysis

    Article Snippet: Diluted cDNA was amplified by quantitative real-time PCR (qPCR) (Applied Biosystems, Foster City, CA, USA) with Power SYBR Green Master Mix (Thermo Fisher, Waltham, MA, USA).

    Techniques: Real-time Polymerase Chain Reaction

    H3K27me3 and LHP1 distribution on FLC. (A) Expression at various developmental stages in wild-type and lif2 plants. Semi-quantitative RT-PCR were performed on seven-day-old in vitro seedlings, rosette leaves after bolting (RL), floral buds just after bolting (FB1) and floral buds after the production of 10 siliques (FB2). The EF-1α gene expression was used as a control. (B) Schematic representation of the FLC locus and the 8 amplified regions used in chromatin immunoprecipitation (ChIP) assays. (C) ChIP analysis to determine the relative level of H3K27me3 at the indicated FLC regions in wild-type and lif2 seedlings. Immunoprecipitated DNA was analyzed by real-time qPCR, and enrichment was calculated as percentage of INPUT. All ChIP experiments were normalized for histone H3 occupancy and normed by using ChIP results on an AGAMOUS control region. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error. (D–F) Complementation of the lhp1 mutant by the expression of the genomic LHP1:MYC-tagged construct. (D) Plant phenotypes, (E) total number of rosette leaves, and (F) protein levels. (G) ChIP assays to determine the relative level of LHP1 binding at the indicated FLC regions in wild-type and lif2 backgrounds expressing the LHP1:MYC-tagged construct. A CONSTANS (CO) region was used as a negative control [23] . Immunoprecipitated DNA was analyzed by real-time qPCR, and enrichment was calculated as percentage of INPUT and normalized relative to a Col-0 control, represented as a dashed line. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error.

    Journal: PLoS ONE

    Article Title: Control of Flowering and Cell Fate by LIF2, an RNA Binding Partner of the Polycomb Complex Component LHP1

    doi: 10.1371/journal.pone.0016592

    Figure Lengend Snippet: H3K27me3 and LHP1 distribution on FLC. (A) Expression at various developmental stages in wild-type and lif2 plants. Semi-quantitative RT-PCR were performed on seven-day-old in vitro seedlings, rosette leaves after bolting (RL), floral buds just after bolting (FB1) and floral buds after the production of 10 siliques (FB2). The EF-1α gene expression was used as a control. (B) Schematic representation of the FLC locus and the 8 amplified regions used in chromatin immunoprecipitation (ChIP) assays. (C) ChIP analysis to determine the relative level of H3K27me3 at the indicated FLC regions in wild-type and lif2 seedlings. Immunoprecipitated DNA was analyzed by real-time qPCR, and enrichment was calculated as percentage of INPUT. All ChIP experiments were normalized for histone H3 occupancy and normed by using ChIP results on an AGAMOUS control region. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error. (D–F) Complementation of the lhp1 mutant by the expression of the genomic LHP1:MYC-tagged construct. (D) Plant phenotypes, (E) total number of rosette leaves, and (F) protein levels. (G) ChIP assays to determine the relative level of LHP1 binding at the indicated FLC regions in wild-type and lif2 backgrounds expressing the LHP1:MYC-tagged construct. A CONSTANS (CO) region was used as a negative control [23] . Immunoprecipitated DNA was analyzed by real-time qPCR, and enrichment was calculated as percentage of INPUT and normalized relative to a Col-0 control, represented as a dashed line. Data in the graphs are the average of at least two qPCR assays from three independent ChIP experiments; the bars represent standard error.

    Article Snippet: Quantitative real-time PCR (qPCR) were performed on Eppendorf Mastercycler® ep realplex (Eppendorf) using MESA FAST qPCR MasterMix Plus for SYBR® Assay (Eurogentec) as manufacturer's instructions.

    Techniques: Expressing, Quantitative RT-PCR, In Vitro, Amplification, Chromatin Immunoprecipitation, Immunoprecipitation, Real-time Polymerase Chain Reaction, Mutagenesis, Construct, Binding Assay, Negative Control

    Co-occupancy of ZNF274, KAP1 and SETDB1 at a ZNF 3′ end in vivo. A) ChIP-qPCR confirmation of a set of ZNF274 targets. Quantitative real-time PCR (qPCR) for 10 target regions identified by ChIP-seq and three negative regions (GAPDH, CDH1, and ZNF44) was performed. The fold enrichment of each site was calculated as 2 to the power of the cycle threshold (cT) difference between input chromatin and ChIP samples. The results in the graph are the mean of three independent replicates with standard deviation. Primers used in these experiments can be found in Supplementary Table S5 . B) Sequential chromatin immunoprecipitation of ZNF274 and KAP1 in K562 cells. ZNF274 or KAP1 ChIP samples were sequentially immunoprecipitated using the indicated antibodies. The samples were analyzed by PCR and agarose gel electrophoresis with ethidium bromide staining using specific primer sets to ZNF180 , a zinc finger gene bound by ZNF274; ZNF555, a zinc finger gene not bound by ZNF274, but bound by KAP1; STX16 , and a non-zinc finger gene bound by neither ZNF274 nor KAP1.

    Journal: PLoS ONE

    Article Title: ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3? Ends of ZNF Genes

    doi: 10.1371/journal.pone.0015082

    Figure Lengend Snippet: Co-occupancy of ZNF274, KAP1 and SETDB1 at a ZNF 3′ end in vivo. A) ChIP-qPCR confirmation of a set of ZNF274 targets. Quantitative real-time PCR (qPCR) for 10 target regions identified by ChIP-seq and three negative regions (GAPDH, CDH1, and ZNF44) was performed. The fold enrichment of each site was calculated as 2 to the power of the cycle threshold (cT) difference between input chromatin and ChIP samples. The results in the graph are the mean of three independent replicates with standard deviation. Primers used in these experiments can be found in Supplementary Table S5 . B) Sequential chromatin immunoprecipitation of ZNF274 and KAP1 in K562 cells. ZNF274 or KAP1 ChIP samples were sequentially immunoprecipitated using the indicated antibodies. The samples were analyzed by PCR and agarose gel electrophoresis with ethidium bromide staining using specific primer sets to ZNF180 , a zinc finger gene bound by ZNF274; ZNF555, a zinc finger gene not bound by ZNF274, but bound by KAP1; STX16 , and a non-zinc finger gene bound by neither ZNF274 nor KAP1.

    Article Snippet: Quantitative real-time PCR Quantitative real-time PCR (qPCR) was performed on a Bio-Rad DNA Engine Opticon Real-Time PCR System using SYBR® Green Master PCR Mix according to the manufacturer's instructions (Invitrogen).

    Techniques: In Vivo, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Immunoprecipitation, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining

    CENP-A chromatin has the physical characteristics of nucleosomes. (A) Experimental design for the separation of in vitro–reconstituted octameric nucleosomes or tetrasomes over a 5–25% sucrose gradient. (B) After sedimentation of in vitro–reconstituted H3 or CENP-A octameric nucleosomes or (CENP-A/H4) 2 or (H3/H4) 2 tetrasomes, fractions were immunoblotted for CENP-A or H3. (C) Experimental design for the sedimentation of in vivo bulk nucleosomes and short polynucleosomes at different points of the cell cycle. (D) Moderate MNase digestion profile of bulk chromatin from random cycling (RC) cells expressing CENP-A TAP or H3.1 TAP . (E) Sucrose gradient sedimentation and fractionation of bulk nucleosomes from CENP-A TAP –expressing cells synchronized at G1, G2, and mitosis. (top) Ethidium bromide stained DNA agarose gel revealing the DNA length extracted from the different fractions. (bottom) Immunoblot for CENP-A TAP . (F) Real-time quantitative PCR for α-satellite DNA in the different fractions (colored). Second axis shows quantification of CENP-A immunoblot shown in E. No CENP-A or α-satellite DNA was detected in fractions 7 and 9.

    Journal: The Journal of Cell Biology

    Article Title: Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points

    doi: 10.1083/jcb.201608083

    Figure Lengend Snippet: CENP-A chromatin has the physical characteristics of nucleosomes. (A) Experimental design for the separation of in vitro–reconstituted octameric nucleosomes or tetrasomes over a 5–25% sucrose gradient. (B) After sedimentation of in vitro–reconstituted H3 or CENP-A octameric nucleosomes or (CENP-A/H4) 2 or (H3/H4) 2 tetrasomes, fractions were immunoblotted for CENP-A or H3. (C) Experimental design for the sedimentation of in vivo bulk nucleosomes and short polynucleosomes at different points of the cell cycle. (D) Moderate MNase digestion profile of bulk chromatin from random cycling (RC) cells expressing CENP-A TAP or H3.1 TAP . (E) Sucrose gradient sedimentation and fractionation of bulk nucleosomes from CENP-A TAP –expressing cells synchronized at G1, G2, and mitosis. (top) Ethidium bromide stained DNA agarose gel revealing the DNA length extracted from the different fractions. (bottom) Immunoblot for CENP-A TAP . (F) Real-time quantitative PCR for α-satellite DNA in the different fractions (colored). Second axis shows quantification of CENP-A immunoblot shown in E. No CENP-A or α-satellite DNA was detected in fractions 7 and 9.

    Article Snippet: Quantitative real-time PCR (qPCR) Quantitative real-time PCR (qPCR) was performed using SYBR Green mix (Bio-Rad Laboratories) with CFX384 Bio Rad Laboratories Real Time System.

    Techniques: In Vitro, Sedimentation, In Vivo, Expressing, Fractionation, Staining, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction

    Quantitative PCR analysis of MTSS1 expression in human oesophageal tissues . (A) Tumour versus normal background tissues; (B) Tumour grade; (C) Tumour-node-metastasis classification; (D) Node status; (E) A two-way division of the patients based on the expression levels of MTSS1 yield a significant correlation with overall survival; (F) A three-way division of the patients based on the expression levels of MTSS1 yield a significant correlation with overall survival; (G) Overall survival analysis in node negative patients; (H) Overall survival analysis in node positive patient.

    Journal: Journal of Translational Medicine

    Article Title: The impact of Metastasis Suppressor-1, MTSS1, on oesophageal squamous cell carcinoma and its clinical significance

    doi: 10.1186/1479-5876-9-95

    Figure Lengend Snippet: Quantitative PCR analysis of MTSS1 expression in human oesophageal tissues . (A) Tumour versus normal background tissues; (B) Tumour grade; (C) Tumour-node-metastasis classification; (D) Node status; (E) A two-way division of the patients based on the expression levels of MTSS1 yield a significant correlation with overall survival; (F) A three-way division of the patients based on the expression levels of MTSS1 yield a significant correlation with overall survival; (G) Overall survival analysis in node negative patients; (H) Overall survival analysis in node positive patient.

    Article Snippet: Quantitative real time PCR Real time quantitative PCR (QPCR) was performed on the Icycler IQ5 system (Bio-Rad, Hammel Hemstead, UK) to quantify the level of MTSS1 transcripts in the oesophageal squamous cell carcinoma specimens (shown as copies/μl from internal standard).

    Techniques: Real-time Polymerase Chain Reaction, Expressing

    q-PCR analyses of 16S rRNA , bph and C230 abundances in myco-augmented microcosms and respective controls . Semi-logarithmic plots of time dependent changes in the relative amount of 16S rRNA (A) bph (B), C230 (C) qPCR-amplified genes in the incubation control and Lentinus tigrinus microcosms in the absence ( i.e ., ICM and Lt M respectively) and in the presence of 2.5% (w/w) soybean oil ( i.e ., ICSOM and Lt SOM). Data are expressed as fold with respect to the relative zero time-point (please, see Materials and Methods).

    Journal: Microbial Cell Factories

    Article Title: Bioaugmentation of a historically contaminated soil by polychlorinated biphenyls with Lentinus tigrinus

    doi: 10.1186/1475-2859-11-35

    Figure Lengend Snippet: q-PCR analyses of 16S rRNA , bph and C230 abundances in myco-augmented microcosms and respective controls . Semi-logarithmic plots of time dependent changes in the relative amount of 16S rRNA (A) bph (B), C230 (C) qPCR-amplified genes in the incubation control and Lentinus tigrinus microcosms in the absence ( i.e ., ICM and Lt M respectively) and in the presence of 2.5% (w/w) soybean oil ( i.e ., ICSOM and Lt SOM). Data are expressed as fold with respect to the relative zero time-point (please, see Materials and Methods).

    Article Snippet: Quantitative real-time PCR assays Quantitative real-time PCR (qPCR) was performed on an iCycler IQ (BioRad, Hercules, CA) using the SYBR Green JumpStart™ Taq ReadyMix™ (Sigma, Milan, Italy) following the manufacturer's instruction.

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

    Mouse-adapted NS1 mutations enhance viral mRNA production in mouse cells in vitro . Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or rHK-wt virus, and total RNA isolated at 8 hpi was reverse transcribed using primers specific for viral mRNA. Real-time PCR (qPCR) was performed to quantify NP, M1 and NS1 viral mRNA levels. Results were normalized by β-actin levels, and presented as values relative to rHK-wt mRNA levels. Data represent the means ± SD (two-tailed student's paired t-test) for NP, NS1 and M1 mRNA relative levels (indicated by bracket) or two-tailed student's t-test for individual mRNA relative values (i p

    Journal: PLoS ONE

    Article Title: Multifunctional Adaptive NS1 Mutations Are Selected upon Human Influenza Virus Evolution in the Mouse

    doi: 10.1371/journal.pone.0031839

    Figure Lengend Snippet: Mouse-adapted NS1 mutations enhance viral mRNA production in mouse cells in vitro . Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or rHK-wt virus, and total RNA isolated at 8 hpi was reverse transcribed using primers specific for viral mRNA. Real-time PCR (qPCR) was performed to quantify NP, M1 and NS1 viral mRNA levels. Results were normalized by β-actin levels, and presented as values relative to rHK-wt mRNA levels. Data represent the means ± SD (two-tailed student's paired t-test) for NP, NS1 and M1 mRNA relative levels (indicated by bracket) or two-tailed student's t-test for individual mRNA relative values (i p

    Article Snippet: Real-time PCR (qPCR) was performed with SYBR GreenER qPCR SuperMix (Bio-Rad Laboratories (Canada) Ltd., Mississuaga, Ontario) and the Bio-Rad Chromo 4 Real-Time PCR Detector (Bio-Rad Laboratories (Canada) Ltd., Mississuaga, Ontario).

    Techniques: In Vitro, Infection, Isolation, Real-time Polymerase Chain Reaction, Two Tailed Test

    2.6. Quantitative PCR analysis of olfactory genes

    Journal: Aquatic toxicology (Amsterdam, Netherlands)

    Article Title: Effects of cadmium on olfactory mediated behaviors and molecular biomarkers in coho salmon (Oncorhynchus kisutch)

    doi: 10.1016/j.aquatox.2013.06.010

    Figure Lengend Snippet: 2.6. Quantitative PCR analysis of olfactory genes

    Article Snippet: Quantitative real time PCR (qPCR) primers were obtained from Eurofins MWG Operon (Huntsville, AL).

    Techniques: Real-time Polymerase Chain Reaction

    Polysome-profiling to identify ISG mRNAs subject to mTOR-dependent translational control. (A) RNA isolated from WISH cells treated with IFN β (100pM) in combination with DMSO or 1μM Torin1 for 12 hrs was subjected to comparative genome-wide mRNA expression profiling, and genes showing differential translation were identified using anota. Genes are plotted according to changes (Δ) in cytoplasmic and polysomal mRNA levels upon the addition of Torin1 to IFN β-treated cells. Genes showing repressed (blue) and enhanced (orange) mRNA translation in response to Torin1 are indicated. (B) Correlation between Torin1 (square)- and rapamycin (triangle)-induced mRNA translation changes (Δ) in IFN β-treated cells. Genes identified in either comparison that show increased (yellow) or decreased (blue) translation are indicated by condition where they were identified (squares or triangles). (C) A lack of correlation is observed when Torin1-induced mRNA translation changes (y-axis) and IFN β-induced cytoplasmic mRNA changes (x-axis) are plotted for all assessed genes. (D) NT5C3A mRNA variants 3 and 4 are transcriptionally induced by IFN. Schematic representation of NT5C3A mRNA variant-specific PCR primers used for qPCR. Arrows represent forward and reverse primers. mRNA abundance in nanograms (ng) was assessed by quantitative polymerase chain reaction (qPCR) for the indicated genes, including mRNA variants 1–4 of NT5C3A . Shown are means +/- standard deviations (n = 3). Theoretical transcriptional start sites (arrows) based on NCBI reference sequences are shown (box). (E) Cytoplasmic and polysomal mRNA abundance (ng) was assessed by qPCR for the indicated genes. Shown are means +/- standard deviations (n = 3). * indicates p-values

    Journal: PLoS ONE

    Article Title: Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes

    doi: 10.1371/journal.pone.0133482

    Figure Lengend Snippet: Polysome-profiling to identify ISG mRNAs subject to mTOR-dependent translational control. (A) RNA isolated from WISH cells treated with IFN β (100pM) in combination with DMSO or 1μM Torin1 for 12 hrs was subjected to comparative genome-wide mRNA expression profiling, and genes showing differential translation were identified using anota. Genes are plotted according to changes (Δ) in cytoplasmic and polysomal mRNA levels upon the addition of Torin1 to IFN β-treated cells. Genes showing repressed (blue) and enhanced (orange) mRNA translation in response to Torin1 are indicated. (B) Correlation between Torin1 (square)- and rapamycin (triangle)-induced mRNA translation changes (Δ) in IFN β-treated cells. Genes identified in either comparison that show increased (yellow) or decreased (blue) translation are indicated by condition where they were identified (squares or triangles). (C) A lack of correlation is observed when Torin1-induced mRNA translation changes (y-axis) and IFN β-induced cytoplasmic mRNA changes (x-axis) are plotted for all assessed genes. (D) NT5C3A mRNA variants 3 and 4 are transcriptionally induced by IFN. Schematic representation of NT5C3A mRNA variant-specific PCR primers used for qPCR. Arrows represent forward and reverse primers. mRNA abundance in nanograms (ng) was assessed by quantitative polymerase chain reaction (qPCR) for the indicated genes, including mRNA variants 1–4 of NT5C3A . Shown are means +/- standard deviations (n = 3). Theoretical transcriptional start sites (arrows) based on NCBI reference sequences are shown (box). (E) Cytoplasmic and polysomal mRNA abundance (ng) was assessed by qPCR for the indicated genes. Shown are means +/- standard deviations (n = 3). * indicates p-values

    Article Snippet: Quantitative real time PCR (qPCR) TRIzol (Invitrogen)-isolated RNA was cleaned using RNeasy Mini Kit (Qiagen 74104) according to manufacturer's instructions including RNase-Free DNase Set (Qiagen 79254) on column DNase digestion.

    Techniques: Isolation, Genome Wide, Expressing, Variant Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    p63 is significantly down-regulated in UM cell lines. ( A ) Representative western blot showing relative protein levels of endogenous p63 protein in UM cell lysates. Skin cell lysate served as a positive control for p63 antibody. ( B ) mRNA was extracted from non-transfected (NT) OCM-1 as well as from A431 cells and p63-tGFP-transfected OCM-1 cells used as positive controls for p63 expression. Quantitative PCR was performed to assess mRNA levels by analysing the amplification plots and dissociation curves for each of the three types of cells. NTC, non-template control.

    Journal: British Journal of Cancer

    Article Title: p63 is required beside p53 for PERP-mediated apoptosis in uveal melanoma

    doi: 10.1038/bjc.2016.269

    Figure Lengend Snippet: p63 is significantly down-regulated in UM cell lines. ( A ) Representative western blot showing relative protein levels of endogenous p63 protein in UM cell lysates. Skin cell lysate served as a positive control for p63 antibody. ( B ) mRNA was extracted from non-transfected (NT) OCM-1 as well as from A431 cells and p63-tGFP-transfected OCM-1 cells used as positive controls for p63 expression. Quantitative PCR was performed to assess mRNA levels by analysing the amplification plots and dissociation curves for each of the three types of cells. NTC, non-template control.

    Article Snippet: Real-time quantitative PCR (qPCR) was performed with gene-specific primer sets for PERP, p63 and GAPDH ( ) using a Stratagene MX3000P qPCR System (Stratagene, La Jolla, CA, USA) and MESA Blue qPCR Kit for SYBR Green assay (Eurogentec, Southampton, UK) according to the manufacturer's instructions.

    Techniques: Western Blot, Positive Control, Transfection, Expressing, Real-time Polymerase Chain Reaction, Amplification

    Thymic reconstitution is not dependent on the stem cell source employed or GvHD occurrence. Mean (±SE) number of log10 TREC was measured by quantitative PCR, before, and 3 and 6 months after transplantation in patients that received either a haploidentical hematopoietic Stem Cell Transplantation (Haplo, N = 33) or a Cord Blood Unrelated Donor Graft (CB, N = 24). Signal Joint (sj) TREC were quantified in ( A,C,E, and F ) and betaTREC in ( B and D ). Results were expressed by 150,000 Peripheral Blood Mononuclear Cells in ( A and B ) and by μL of blood in ( C,D,E, and F ). Patients were subsequently subdivided according to GvHD occurrence ( E and F ).

    Journal: Frontiers in Immunology

    Article Title: Thymic function recovery after unrelated donor cord blood or T-cell depleted HLA-haploidentical stem cell transplantation correlates with leukemia relapse

    doi: 10.3389/fimmu.2013.00054

    Figure Lengend Snippet: Thymic reconstitution is not dependent on the stem cell source employed or GvHD occurrence. Mean (±SE) number of log10 TREC was measured by quantitative PCR, before, and 3 and 6 months after transplantation in patients that received either a haploidentical hematopoietic Stem Cell Transplantation (Haplo, N = 33) or a Cord Blood Unrelated Donor Graft (CB, N = 24). Signal Joint (sj) TREC were quantified in ( A,C,E, and F ) and betaTREC in ( B and D ). Results were expressed by 150,000 Peripheral Blood Mononuclear Cells in ( A and B ) and by μL of blood in ( C,D,E, and F ). Patients were subsequently subdivided according to GvHD occurrence ( E and F ).

    Article Snippet: Quantification of sjTREC and beta-TREC was performed by real-time quantitative PCR (qPCR) (ABIPRISM7500, Applied Biosystems, Foster City, CA), as previously described (Clave et al., ).

    Techniques: Real-time Polymerase Chain Reaction, Transplantation Assay

    UPR target gene activation precedes Tm-induced steatosis. (A–C) Larvae were treated starting on 3 dpf with DMSO and 0.25 μg/ml Tm and collected at the indicated time points. At least 15 larvae were stained with Oil Red O and scored for steatosis (A) and at least 5 livers were dissected for RNA extraction (B,C). (A) The log odds ratio of steatosis was plotted versus time (see Materials and Methods and supplementary material Table S3 ). (B) UPR target gene analysis measured by qPCR in liver cDNAs from the same cohorts assessed for steatosis in A. Expression of each gene is plotted as log fold change (log FC) over time (see Materials and Methods and supplementary material Table S7 ). (C) PCR analysis of xbp1 splicing with the percentage of spliced/total xbp1 for each sample plotted ( n =2). * P

    Journal: Disease Models & Mechanisms

    Article Title: Molecularly defined unfolded protein response subclasses have distinct correlations with fatty liver disease in zebrafish

    doi: 10.1242/dmm.014472

    Figure Lengend Snippet: UPR target gene activation precedes Tm-induced steatosis. (A–C) Larvae were treated starting on 3 dpf with DMSO and 0.25 μg/ml Tm and collected at the indicated time points. At least 15 larvae were stained with Oil Red O and scored for steatosis (A) and at least 5 livers were dissected for RNA extraction (B,C). (A) The log odds ratio of steatosis was plotted versus time (see Materials and Methods and supplementary material Table S3 ). (B) UPR target gene analysis measured by qPCR in liver cDNAs from the same cohorts assessed for steatosis in A. Expression of each gene is plotted as log fold change (log FC) over time (see Materials and Methods and supplementary material Table S7 ). (C) PCR analysis of xbp1 splicing with the percentage of spliced/total xbp1 for each sample plotted ( n =2). * P

    Article Snippet: Real time quantitative PCR (qPCR) was performed using the PerfeCTa SYBR Green FastMix kit (Quanta Biosciences) and the Roche LightCycler 480 System.

    Techniques: Activation Assay, Staining, RNA Extraction, Real-time Polymerase Chain Reaction, Expressing, Polymerase Chain Reaction

    BFA, Tg and Tm differentially induce UPR sensors in the liver. (A,B) Standard PCR (A) and qPCR (B) analysis of xbp1 splicing in the livers of fish treated from 3 to 5 dpf with DMSO, 1 μg/ml BFA, 0.75 μM Tg or 1 μg/ml Tm using primers that amplify both unspliced (- u ) and spliced (- s ) xbp1 . The average ratio of xbp1-second to xbp1-t is indicated ( n =2). (C) Protein extracts from livers dissected from 5-dpf larvae treated as in A were blotted with anti- P-Eif2a and anti- tubulin as a loading control. Quantification and normalization to tubulin and DMSO controls is shown ( n =2). (D) Analysis of atf4 and atf6 expression in livers of fish treated as in A. In B and D, target gene expression was normalized to rpp0 and fold changes compared to DMSO are plotted; n =13 for DMSO, 10 for Tm, 8 for Tg and 6 for BFA. Bars represent standard error in all graphs. * P

    Journal: Disease Models & Mechanisms

    Article Title: Molecularly defined unfolded protein response subclasses have distinct correlations with fatty liver disease in zebrafish

    doi: 10.1242/dmm.014472

    Figure Lengend Snippet: BFA, Tg and Tm differentially induce UPR sensors in the liver. (A,B) Standard PCR (A) and qPCR (B) analysis of xbp1 splicing in the livers of fish treated from 3 to 5 dpf with DMSO, 1 μg/ml BFA, 0.75 μM Tg or 1 μg/ml Tm using primers that amplify both unspliced (- u ) and spliced (- s ) xbp1 . The average ratio of xbp1-second to xbp1-t is indicated ( n =2). (C) Protein extracts from livers dissected from 5-dpf larvae treated as in A were blotted with anti- P-Eif2a and anti- tubulin as a loading control. Quantification and normalization to tubulin and DMSO controls is shown ( n =2). (D) Analysis of atf4 and atf6 expression in livers of fish treated as in A. In B and D, target gene expression was normalized to rpp0 and fold changes compared to DMSO are plotted; n =13 for DMSO, 10 for Tm, 8 for Tg and 6 for BFA. Bars represent standard error in all graphs. * P

    Article Snippet: Real time quantitative PCR (qPCR) was performed using the PerfeCTa SYBR Green FastMix kit (Quanta Biosciences) and the Roche LightCycler 480 System.

    Techniques: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Fluorescence In Situ Hybridization, Expressing

    Characterization of HHV-6 reactivation. a Trichostatin A (TSA) induced histone acetylation in U2OS cells. TSA (80 ng/ml) was added to U2OS cell culture media for 24 h to induce histone acetylation. Total protein was extracted and used for immunoblotting. Histone H4 pan acetylation (H4ac), Histone 3 K27 acetylation (H3K27ac), Histone 3 K27 methylation (H3K27me) and Histone 3 K4 methylation (H3K4me) were studied using specific antibodies. Actin was used as loading control. U2OS cells without HHV-6 (-HHV-6A) were used as control. b TSA treatment induced expression of RFP in latent HHV-6A carrying U2OS cells. Microscopic evaluation was carried out for RFP expression in U2OS cells carrying latent HHV-6A. Cells were treated with DMSO in parallel as a solvent control. c TSA-induced HHV-6A reactivation was quantified by qRT-PCR analysis of two early viral transcripts (p41 and U86). U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA for three different time intervals. Total RNA was extracted and were used for cDNA synthesis and subsequent RT-PCR. Data represent the mean ± SEM of three independent experiments. dpi, days post infection. d Immunoprecipitation (IP) of HHV-6 IE2 protein was carried out to test immediate early protein synthesis. U2OS cells carrying latent HHV-6A were treated with DMSO or TSA for 2 days. Total cell lysates were extracted and used for immunopreciptation. A smaller ~ 55 kDa fraction of IE2 was detected in IP. e Viral DNA replication was studied by qPCR. U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA or DMSO for two different time intervals. Total genomic DNA was extracted and were used for qPCR analysis. Data represent the mean ± SEM of three independent experiments. dpi, days post infection. f Detection of several different HHV-6A encoded small non-coding RNAs by Northern hybridization. U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA (T) or DMSO (D) for 48 h. 10 μg of total RNA were separated on a denaturing Urea gel for Northern hybridization. Decade marker (DM) was used to verify sizes of identified RNA. Transcription of previously described small non-coding RNAs (labeled as sR) was tested using specific DNA probes. Human U6 RNA was used as loading control. g Detection of newly identified HHV-6A encoded sncRNA-U73 by Northern hybridization as described in figure f. h Sequence details of newly identified sncRNA-U73. Genomic location of the sncRNA-U73 is indicated as mapped to HHV-6A U1102 genome (Genebank X83413.2). All blots or gels ( a , d , f and g ) derive from the same experiment and they were processed in parallel

    Journal: NPJ Genomic Medicine

    Article Title: HHV-6 encoded small non-coding RNAs define an intermediate and early stage in viral reactivation

    doi: 10.1038/s41525-018-0064-5

    Figure Lengend Snippet: Characterization of HHV-6 reactivation. a Trichostatin A (TSA) induced histone acetylation in U2OS cells. TSA (80 ng/ml) was added to U2OS cell culture media for 24 h to induce histone acetylation. Total protein was extracted and used for immunoblotting. Histone H4 pan acetylation (H4ac), Histone 3 K27 acetylation (H3K27ac), Histone 3 K27 methylation (H3K27me) and Histone 3 K4 methylation (H3K4me) were studied using specific antibodies. Actin was used as loading control. U2OS cells without HHV-6 (-HHV-6A) were used as control. b TSA treatment induced expression of RFP in latent HHV-6A carrying U2OS cells. Microscopic evaluation was carried out for RFP expression in U2OS cells carrying latent HHV-6A. Cells were treated with DMSO in parallel as a solvent control. c TSA-induced HHV-6A reactivation was quantified by qRT-PCR analysis of two early viral transcripts (p41 and U86). U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA for three different time intervals. Total RNA was extracted and were used for cDNA synthesis and subsequent RT-PCR. Data represent the mean ± SEM of three independent experiments. dpi, days post infection. d Immunoprecipitation (IP) of HHV-6 IE2 protein was carried out to test immediate early protein synthesis. U2OS cells carrying latent HHV-6A were treated with DMSO or TSA for 2 days. Total cell lysates were extracted and used for immunopreciptation. A smaller ~ 55 kDa fraction of IE2 was detected in IP. e Viral DNA replication was studied by qPCR. U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA or DMSO for two different time intervals. Total genomic DNA was extracted and were used for qPCR analysis. Data represent the mean ± SEM of three independent experiments. dpi, days post infection. f Detection of several different HHV-6A encoded small non-coding RNAs by Northern hybridization. U2OS cells carrying latent HHV-6A were treated with 80 ng/ml of TSA (T) or DMSO (D) for 48 h. 10 μg of total RNA were separated on a denaturing Urea gel for Northern hybridization. Decade marker (DM) was used to verify sizes of identified RNA. Transcription of previously described small non-coding RNAs (labeled as sR) was tested using specific DNA probes. Human U6 RNA was used as loading control. g Detection of newly identified HHV-6A encoded sncRNA-U73 by Northern hybridization as described in figure f. h Sequence details of newly identified sncRNA-U73. Genomic location of the sncRNA-U73 is indicated as mapped to HHV-6A U1102 genome (Genebank X83413.2). All blots or gels ( a , d , f and g ) derive from the same experiment and they were processed in parallel

    Article Snippet: Quantitative real time PCR Quantitative PCR (qPCR) was performed using PerfeCTa qPCR SuperMix (Quanta Biosciences) on a StepOnePlus real time PCR platform (Applied Biosciences) using manufacturer’s protocol and SYBR Green chemistry.

    Techniques: Cell Culture, Methylation, Expressing, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, Infection, Immunoprecipitation, Real-time Polymerase Chain Reaction, Northern Blot, Hybridization, Marker, Labeling, Sequencing

    Part of the promoter sequence of UBC and the primer sequence of UBC_3 (depicted bold and underlined). The qPCR fragment is located around the transcription start site (CTG, italic underlined), starting from 31 bp upstream of the 5′-UTR (Untranslated Region) to 155 bp into this region and 553 bp upstream of the translation start codon (ATG, italic underlined). In the PCR fragment of the UBC_3 primers there are 14 CpG sites, of which one or more have differential methylation.

    Journal: Scientific Reports

    Article Title: Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model

    doi: 10.1038/srep20837

    Figure Lengend Snippet: Part of the promoter sequence of UBC and the primer sequence of UBC_3 (depicted bold and underlined). The qPCR fragment is located around the transcription start site (CTG, italic underlined), starting from 31 bp upstream of the 5′-UTR (Untranslated Region) to 155 bp into this region and 553 bp upstream of the translation start codon (ATG, italic underlined). In the PCR fragment of the UBC_3 primers there are 14 CpG sites, of which one or more have differential methylation.

    Article Snippet: Quantitative real-time PCR (qPCR) Quantitative real-time PCR (qRT-PCR) measurements were performed in triplicate using the LightCycler480 qPCR machine (Roche Applied Science, Penzberg, Germany).

    Techniques: Sequencing, Real-time Polymerase Chain Reaction, CTG Assay, Polymerase Chain Reaction, Methylation

    Comparison of ARMS-PCR and qPCR assays. Ten cases shown to be positive for the JAK2 V617F mutation using ARMS-PCR exhibited an allele burden of 55% ±9% (mean ± SE) according to qPCR. Ten negative cases according to ARMS-PCR showed an allele burden of 1.9% ±0.6%, including two cases that were negative by ARMS-PCR and positive by qPCR with a value above our cutoff ( > 3.65%, estimated from a healthy population).

    Journal: PLoS ONE

    Article Title: Improved Diagnosis of the Transition to JAK2V617F Homozygosity: The Key Feature for Predicting the Evolution of Myeloproliferative Neoplasms

    doi: 10.1371/journal.pone.0086401

    Figure Lengend Snippet: Comparison of ARMS-PCR and qPCR assays. Ten cases shown to be positive for the JAK2 V617F mutation using ARMS-PCR exhibited an allele burden of 55% ±9% (mean ± SE) according to qPCR. Ten negative cases according to ARMS-PCR showed an allele burden of 1.9% ±0.6%, including two cases that were negative by ARMS-PCR and positive by qPCR with a value above our cutoff ( > 3.65%, estimated from a healthy population).

    Article Snippet: Quantitative Real-time PCR Quantitative real-time PCR (qPCR) was performed using the LightCycler 2.0 (Roche Diagnostics, Mannheim, Germany), which is based on SYBR Green chemistry.

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

    HT extracts inhibit gene expression. (a–c) Cells were treated with HT extracts at the indicated concentrations and quantitative PCR was performed ( n = 6/group). Data are expressed as means ± SD. ∗ P

    Journal: Evidence-based Complementary and Alternative Medicine : eCAM

    Article Title: Helicteric Acid, Oleanic Acid, and Betulinic Acid, Three Triterpenes from Helicteres angustifolia L., Inhibit Proliferation and Induce Apoptosis in HT-29 Colorectal Cancer Cells via Suppressing NF-κB and STAT3 Signaling

    doi: 10.1155/2017/5180707

    Figure Lengend Snippet: HT extracts inhibit gene expression. (a–c) Cells were treated with HT extracts at the indicated concentrations and quantitative PCR was performed ( n = 6/group). Data are expressed as means ± SD. ∗ P

    Article Snippet: Real-time quantitative PCR (qPCR) was performed to quantify mRNA levels using the SYBR-Green PCR kit (Roche, Indianapolis, IN, USA) on the LightCycler 480 Real-Time PCR System (Roche).

    Techniques: Expressing, Real-time Polymerase Chain Reaction

    Visualization of the PCR product in agarose gel obtained with qPCR virB4 assay for representative strains of Vibrio , i.e., which were tested positive and negative for BRD development after an infection experiment. Lanes MT corresponds to the BenchTop DNA ladder (Promega, Madison, WI, USA). T-H 2 O represents the water negative control.

    Journal: PeerJ

    Article Title: Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams

    doi: 10.7717/peerj.1484

    Figure Lengend Snippet: Visualization of the PCR product in agarose gel obtained with qPCR virB4 assay for representative strains of Vibrio , i.e., which were tested positive and negative for BRD development after an infection experiment. Lanes MT corresponds to the BenchTop DNA ladder (Promega, Madison, WI, USA). T-H 2 O represents the water negative control.

    Article Snippet: Quantitative real-time PCR (qPCR) Real-time PCR was performed on a LightCycler 480 Instrument (Roche Diagnostics, Mannheim, Germany) using LightCycler 480 Probe Master Mix based on Taqman detection (Roche Diagnostics).

    Techniques: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Infection, Negative Control

    CYP24A1 mRNA Expression is Stimulated by SIRT1 and Resveratrol (A) HEK293 cells were transfected with 5 ng pCMV-empty (-SIRT1, -S) or 5 ng pCMV-SIRT1 (+SIRT1, +S) in addition to 50 ng of pSG5-VDR and 250 ng of pTZ18U as carrier DNA. The cells were treated post-transfection with 10 nM 1,25D, 10 nM 1,25D+20 µM EX-527 (EX), or 10 nM 1,25D+25 µM Res. Quantitative PCR was performed on cell lysates and results are presented as a fold-induction after normalizing to human GAPDH. Error bars represent standard deviation. Results are the average of 15 biological replicates (n=15). (B) As in (A) except that cells were treated with ETOH, 10 nM 1,25D, 10 nM 1,25D+20 µM EX-527 (EX), or 10nM 1,25D+25 µM Res. Note that the group treated with EX-527 also received an additional dose of drug during time of transfection to inhibit endogenous SIRT1. Results shown are the average of nine biological replicates (n=9). P-values are noted in the figure panels.

    Journal: The Journal of steroid biochemistry and molecular biology

    Article Title: SIRT1 Enzymatically Potentiates 1,25-Dihydroxyvitamin D3 Signaling via Vitamin D Receptor Deacetylation

    doi: 10.1016/j.jsbmb.2017.06.010

    Figure Lengend Snippet: CYP24A1 mRNA Expression is Stimulated by SIRT1 and Resveratrol (A) HEK293 cells were transfected with 5 ng pCMV-empty (-SIRT1, -S) or 5 ng pCMV-SIRT1 (+SIRT1, +S) in addition to 50 ng of pSG5-VDR and 250 ng of pTZ18U as carrier DNA. The cells were treated post-transfection with 10 nM 1,25D, 10 nM 1,25D+20 µM EX-527 (EX), or 10 nM 1,25D+25 µM Res. Quantitative PCR was performed on cell lysates and results are presented as a fold-induction after normalizing to human GAPDH. Error bars represent standard deviation. Results are the average of 15 biological replicates (n=15). (B) As in (A) except that cells were treated with ETOH, 10 nM 1,25D, 10 nM 1,25D+20 µM EX-527 (EX), or 10nM 1,25D+25 µM Res. Note that the group treated with EX-527 also received an additional dose of drug during time of transfection to inhibit endogenous SIRT1. Results shown are the average of nine biological replicates (n=9). P-values are noted in the figure panels.

    Article Snippet: For quantitative real-time PCR (qPCR), 1.5 µl of cDNA was used in a 10 µl reaction containing 5 µl FastStart Universal SYBR Green Master Mix with Rox (Roche Applied Science, Indianapolis, IN) and appropriate primers.

    Techniques: Expressing, Transfection, Real-time Polymerase Chain Reaction, Standard Deviation

    CuIIb modulated the NF-κB and STAT3 pathways in activated lymphocytes. Cells were pretreated with CuIIb (10 µM) for 1 h, then exposed to Con A for indicated time periods. The phosphorylation of NF-κB/p65, IκB (A) and STAT3 (E) at various time points was determined by Western blotting. β-Tubulin was used as a loading control. Representative western blots are shown in (A and E) and the relative densitometric ratios of each phosphorylated protein to its total protein are shown in (B and F). (C) Immunofluorescence analysis of the distribution of NF-κB/p65 in lymphocytes. After co-treatment with CuIIb and Con A for 1 h, cells were fixed and then immunostained with anti-p65 antibody (red) followed by CF568-labeled second antibody. Nuclei (blue) were revealed by Hochest 33342 staining. Fluorescent images were obtained by fluorescence microscopy with a 100× oil objective lens. Representative of at least 10 images for each group were shown. Scale bar, 5 µm. (D) Quantitative PCR analysis of the mRNA levels of IκBα and TNF-α. CuIIb were pretreated for 1 h prior to stimulation with Con A. Levels of IκBα and TNF-α mRNA were determined 3 h after Con A stimulation. The mRNA levels normalized to β-actin are expressed as mean ± SD with controls defined as 1 (n = 3). * P

    Journal: PLoS ONE

    Article Title: Cucurbitacin IIb Exhibits Anti-Inflammatory Activity through Modulating Multiple Cellular Behaviors of Mouse Lymphocytes

    doi: 10.1371/journal.pone.0089751

    Figure Lengend Snippet: CuIIb modulated the NF-κB and STAT3 pathways in activated lymphocytes. Cells were pretreated with CuIIb (10 µM) for 1 h, then exposed to Con A for indicated time periods. The phosphorylation of NF-κB/p65, IκB (A) and STAT3 (E) at various time points was determined by Western blotting. β-Tubulin was used as a loading control. Representative western blots are shown in (A and E) and the relative densitometric ratios of each phosphorylated protein to its total protein are shown in (B and F). (C) Immunofluorescence analysis of the distribution of NF-κB/p65 in lymphocytes. After co-treatment with CuIIb and Con A for 1 h, cells were fixed and then immunostained with anti-p65 antibody (red) followed by CF568-labeled second antibody. Nuclei (blue) were revealed by Hochest 33342 staining. Fluorescent images were obtained by fluorescence microscopy with a 100× oil objective lens. Representative of at least 10 images for each group were shown. Scale bar, 5 µm. (D) Quantitative PCR analysis of the mRNA levels of IκBα and TNF-α. CuIIb were pretreated for 1 h prior to stimulation with Con A. Levels of IκBα and TNF-α mRNA were determined 3 h after Con A stimulation. The mRNA levels normalized to β-actin are expressed as mean ± SD with controls defined as 1 (n = 3). * P

    Article Snippet: Quantitative PCR Real-time quantitative PCR (qPCR) was performed on Roche’s LightCycler 480 real-time PCR system. qPCR for each sample was performed twice in triplicates using a 20-µl reaction system containing 50 ng initial total RNA.

    Techniques: Western Blot, Immunofluorescence, Labeling, Staining, Fluorescence, Microscopy, Real-time Polymerase Chain Reaction

    Interleukin-4 (IL-4) and melatonin downregulated the expression of intercellular cell adhesion molecule-1 (ICAM-1) induced with D-glucose or interleukin-1β. After D-glucose (30 mM; 48 h incubation) or interleukin-1β (IL-1β; 10 ng/ml; 24 h incubation) induction with or without IL-4 (40 ng/ml) or melatonin (100 μM), total RNA was extracted from the human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells, and the supernatants were harvested for quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA) to measure the levels of ICAM-1 mRNA and protein, respectively. The mRNA and protein levels of ICAM-1 increased significantly after induction with D-glucose or IL-1β, but were significantly downregulated by IL-4 and melatonin. The data are expressed as the mean± standard deviation (SD; n = 4; *p

    Journal: Molecular Vision

    Article Title: Interleukin-4 and melatonin ameliorate high glucose and interleukin-1? stimulated inflammatory reaction in human retinal endothelial cells and retinal pigment epithelial cells

    doi:

    Figure Lengend Snippet: Interleukin-4 (IL-4) and melatonin downregulated the expression of intercellular cell adhesion molecule-1 (ICAM-1) induced with D-glucose or interleukin-1β. After D-glucose (30 mM; 48 h incubation) or interleukin-1β (IL-1β; 10 ng/ml; 24 h incubation) induction with or without IL-4 (40 ng/ml) or melatonin (100 μM), total RNA was extracted from the human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells, and the supernatants were harvested for quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA) to measure the levels of ICAM-1 mRNA and protein, respectively. The mRNA and protein levels of ICAM-1 increased significantly after induction with D-glucose or IL-1β, but were significantly downregulated by IL-4 and melatonin. The data are expressed as the mean± standard deviation (SD; n = 4; *p

    Article Snippet: Quantitative real-time PCR (qPCR) was conducted on an ABI Prism 7000 system with a SYBR Green PCR kit (TaKaRa) by denaturing at 95 °C for 5 min, followed by 40 cycles of denaturation at 95 °C, annealing at 60 °C, and extension at 72 °C for 10 s, respectively.

    Techniques: Expressing, Incubation, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Standard Deviation

    Interleukin-4 (IL-4) and melatonin downregulated the expression of vascular endothelial growth factor (VEGF). Human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells were cultured to a state of subconfluency and then maintained in human endothelial-serum free medium (HE-SFM) or Dulbecco’s Modified Eagle Medium (DMEM) that contained 1% serum for 24 h for synchronization. The cells were then exposed to D-glucose (30 mM; 48 h incubation) or interleukin-1β (IL-1β; 10 ng/ml; 24 h incubation) in the presence or absence of IL-4 (40 ng/ml) or melatonin (100 μM). Total RNA was extracted, and the supernatants were harvested. VEGF expression was analyzed using quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The data are expressed as the mean±standard deviation (SD; n = 4; *p

    Journal: Molecular Vision

    Article Title: Interleukin-4 and melatonin ameliorate high glucose and interleukin-1? stimulated inflammatory reaction in human retinal endothelial cells and retinal pigment epithelial cells

    doi:

    Figure Lengend Snippet: Interleukin-4 (IL-4) and melatonin downregulated the expression of vascular endothelial growth factor (VEGF). Human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells were cultured to a state of subconfluency and then maintained in human endothelial-serum free medium (HE-SFM) or Dulbecco’s Modified Eagle Medium (DMEM) that contained 1% serum for 24 h for synchronization. The cells were then exposed to D-glucose (30 mM; 48 h incubation) or interleukin-1β (IL-1β; 10 ng/ml; 24 h incubation) in the presence or absence of IL-4 (40 ng/ml) or melatonin (100 μM). Total RNA was extracted, and the supernatants were harvested. VEGF expression was analyzed using quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The data are expressed as the mean±standard deviation (SD; n = 4; *p

    Article Snippet: Quantitative real-time PCR (qPCR) was conducted on an ABI Prism 7000 system with a SYBR Green PCR kit (TaKaRa) by denaturing at 95 °C for 5 min, followed by 40 cycles of denaturation at 95 °C, annealing at 60 °C, and extension at 72 °C for 10 s, respectively.

    Techniques: Expressing, Cell Culture, Modification, Incubation, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Standard Deviation

    Interleukin-4 (IL-4) and melatonin downregulated the expression of matrix metalloproteinases 2 (MMP2) and matrix metalloproteinases 9 (MMP9). Human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells were cultured for 24 h (interleukin-1β [IL-1β] stimulation) or 48 h (D-glucose stimulation) with or without IL-4 (40 ng/ml) or melatonin (100 μM). The mRNA and protein levels of the MMP2 and MMP9 genes were analyzed with quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The expression of MMP2 and MMP9 was significantly decreased by IL-4 and melatonin in human RECs and RPE cells induced by D-glucose or IL-1β. The data are expressed as the mean±standard deviation (SD; n = 3; *p

    Journal: Molecular Vision

    Article Title: Interleukin-4 and melatonin ameliorate high glucose and interleukin-1? stimulated inflammatory reaction in human retinal endothelial cells and retinal pigment epithelial cells

    doi:

    Figure Lengend Snippet: Interleukin-4 (IL-4) and melatonin downregulated the expression of matrix metalloproteinases 2 (MMP2) and matrix metalloproteinases 9 (MMP9). Human retinal endothelial cells (RECs) and retinal pigment epithelial (RPE) cells were cultured for 24 h (interleukin-1β [IL-1β] stimulation) or 48 h (D-glucose stimulation) with or without IL-4 (40 ng/ml) or melatonin (100 μM). The mRNA and protein levels of the MMP2 and MMP9 genes were analyzed with quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA), respectively. The expression of MMP2 and MMP9 was significantly decreased by IL-4 and melatonin in human RECs and RPE cells induced by D-glucose or IL-1β. The data are expressed as the mean±standard deviation (SD; n = 3; *p

    Article Snippet: Quantitative real-time PCR (qPCR) was conducted on an ABI Prism 7000 system with a SYBR Green PCR kit (TaKaRa) by denaturing at 95 °C for 5 min, followed by 40 cycles of denaturation at 95 °C, annealing at 60 °C, and extension at 72 °C for 10 s, respectively.

    Techniques: Expressing, Cell Culture, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Standard Deviation

    PCR and qPCR validation of candidate transcripts. (A) PCR amplification (all 36 cycles) of candidate genes from different lines. PDS was used as a positive control. (B) Relative expression levels of green and purple B. juncea ( eEF1B α 2 was used as an internal control). (C) Relative gene expression levels under cold and high light treatment ( eEF1B α 2 was used as an internal control). ** Means statistically significant.

    Journal: Frontiers in Plant Science

    Article Title: Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica

    doi: 10.3389/fpls.2016.01245

    Figure Lengend Snippet: PCR and qPCR validation of candidate transcripts. (A) PCR amplification (all 36 cycles) of candidate genes from different lines. PDS was used as a positive control. (B) Relative expression levels of green and purple B. juncea ( eEF1B α 2 was used as an internal control). (C) Relative gene expression levels under cold and high light treatment ( eEF1B α 2 was used as an internal control). ** Means statistically significant.

    Article Snippet: Real-time quantitative PCR (qPCR) was performed in a MX3000P qPCR system (Agilent).

    Techniques: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Amplification, Positive Control, Expressing

    Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by RT-PCR at 72 h post-infection. ( C ) qPCR results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p

    Journal: Cells

    Article Title: CRISPR/Cas9-Mediated Hitchhike Expression of Functional shRNAs at the Porcine miR-17-92 Cluster

    doi: 10.3390/cells8020113

    Figure Lengend Snippet: Verification of the antiviral ability of TG PFF clones. ( A ) Virus resistance in identified positive PFF clones #31 and #67 was examined by IFA. sh-Con: scrambled shRNA transgenic PFFs. ( B ) Antiviral ability in positive PFF clones #31 and #67 was further assessed by RT-PCR at 72 h post-infection. ( C ) qPCR results showed the copy number of CSFV virus in positive PFF clones #31 and #67. The values displayed on the Y axis are calculated in lg. All values are the mean ± S.E.M., n = 3. *** p

    Article Snippet: Quantitative real time PCR (qPCR) was also performed using a miRcute miRNA qPCR Detection Kit (Tiangen, Beijing, China) according to the manufacturer′s instructions.

    Techniques: Clone Assay, Immunofluorescence, shRNA, Transgenic Assay, Reverse Transcription Polymerase Chain Reaction, Infection, Real-time Polymerase Chain Reaction

    Genomic organization and expression of the p miR-17-92 cluster. ( A ) Schematic representation of the p miR-17-92 cluster. The p miR-17-92 cluster is located in an intergenic region on chromosome 11 in the porcine genome. Pre-miRNAs are indicated as color-coded boxes. Black boxes correspond to the mature miRNA. ( B ) Sequence comparison of the miRNAs expressed from the p miR-17-92 cluster. The seed sequences are indicated in red. ( C ) Polymorphism analysis of the p miR-17-92 cluster in different pig breeds and in two different cell lines. M: DNA marker III. PFFs: porcine fetal fibroblasts from Yorkshire (China) pigs. ( D ) Relative expression of pri-miR-17-92 in different adult porcine tissues as determined by real-time PCR. All values are the mean ± S.E.M., n = 3. ( E) Relative expression of miRNAs expressed from the p miR-17-92 cluster in a variety of tissues as determined by qPCR. All values are the mean ± S.E.M., n = 3.

    Journal: Cells

    Article Title: CRISPR/Cas9-Mediated Hitchhike Expression of Functional shRNAs at the Porcine miR-17-92 Cluster

    doi: 10.3390/cells8020113

    Figure Lengend Snippet: Genomic organization and expression of the p miR-17-92 cluster. ( A ) Schematic representation of the p miR-17-92 cluster. The p miR-17-92 cluster is located in an intergenic region on chromosome 11 in the porcine genome. Pre-miRNAs are indicated as color-coded boxes. Black boxes correspond to the mature miRNA. ( B ) Sequence comparison of the miRNAs expressed from the p miR-17-92 cluster. The seed sequences are indicated in red. ( C ) Polymorphism analysis of the p miR-17-92 cluster in different pig breeds and in two different cell lines. M: DNA marker III. PFFs: porcine fetal fibroblasts from Yorkshire (China) pigs. ( D ) Relative expression of pri-miR-17-92 in different adult porcine tissues as determined by real-time PCR. All values are the mean ± S.E.M., n = 3. ( E) Relative expression of miRNAs expressed from the p miR-17-92 cluster in a variety of tissues as determined by qPCR. All values are the mean ± S.E.M., n = 3.

    Article Snippet: Quantitative real time PCR (qPCR) was also performed using a miRcute miRNA qPCR Detection Kit (Tiangen, Beijing, China) according to the manufacturer′s instructions.

    Techniques: Expressing, Sequencing, Marker, Real-time Polymerase Chain Reaction

    (a) H E staining showing the junction between normal epithelium and severe dysplasia in human papillomavirus ( HPV )‐positive tonsil squa‐mous cell carcinoma (top left). Although some flattening of cells at the apical surface may exist, the majority of the abnormal epithelium has a poorly differentiated dense basaloid appearance with nuclear pleomorphism. MCM 7 (top right) and Ki67 (bottom left) staining are present in more than two‐thirds of the abnormal epithelium. In situ hybridization reveals an elevated level of HPV 16 DNA (bottom right) in the dysplastic epithelium when compared to the normal region (magnification, ×100; inset, ×150; Infinity capture software). ISH , in situ hybridization. (b) Reverse transcription–real‐time quantitative PCR ( RT ‐ qPCR ) analysis for all HPV ‐positive sample types showing significant differential expression of SYCP 2 (log2 fold change, 3.1 [95% confidence interval, 1.8–4.4]; P

    Journal: Cancer Science

    Article Title: Deregulation of SYCP2 predicts early stage human papillomavirus‐positive oropharyngeal carcinoma: A prospective whole transcriptome analysis

    doi: 10.1111/cas.12809

    Figure Lengend Snippet: (a) H E staining showing the junction between normal epithelium and severe dysplasia in human papillomavirus ( HPV )‐positive tonsil squa‐mous cell carcinoma (top left). Although some flattening of cells at the apical surface may exist, the majority of the abnormal epithelium has a poorly differentiated dense basaloid appearance with nuclear pleomorphism. MCM 7 (top right) and Ki67 (bottom left) staining are present in more than two‐thirds of the abnormal epithelium. In situ hybridization reveals an elevated level of HPV 16 DNA (bottom right) in the dysplastic epithelium when compared to the normal region (magnification, ×100; inset, ×150; Infinity capture software). ISH , in situ hybridization. (b) Reverse transcription–real‐time quantitative PCR ( RT ‐ qPCR ) analysis for all HPV ‐positive sample types showing significant differential expression of SYCP 2 (log2 fold change, 3.1 [95% confidence interval, 1.8–4.4]; P

    Article Snippet: Whole transcriptome analysis used the Illumina Genome Analyzer IIx machine (HumanHT‐12 version 4 BeadChip; Illumina, San Diego, CA, USA) and the results were validated with RT–quantitative real‐time PCR (RT‐qPCR) (ViiA 7; Applied Biosystems, Hampton, NH, USA).

    Techniques: Staining, In Situ Hybridization, Software, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Expressing