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    Thermo Fisher taqman universal pcr master mix
    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex <t>PCR</t> NoROX Master Mix (Qiagen), ( B ) <t>TaqMan®</t> Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).
    Taqman Universal Pcr Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 54482 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taqman universal pcr master mix/product/Thermo Fisher
    Average 99 stars, based on 54482 article reviews
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    taqman universal pcr master mix - by Bioz Stars, 2020-07
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    99
    Thermo Fisher pcr master mix
    Estimation of linear range of phage particles by phage <t>PCR.</t> (a) Real-time PCR amplification of 10-fold serial dilutions of phage particles in water. Five μl of each preparation was mixed with 15 μl of PCR pre mix containing primers specific to the arabinose promoter of the phagemid vector and the <t>5’-FAM</t> probe. (b) Standard curve of the phage PCR obtained by plotting the threshold Ct value of each dilution against the log number of phage particles added to the PCR pre mix. Each data point refers to an average of two replicates (c) Titration of 3-PBA phage particles forming the antibody-alalyte-phage complex in the PHAIA plate. The phage particles were recovered from PHAIA wells incubated with 0, 1, 5, and 25 ng/ml of 3-PBA. Each column represents the mean value of three replicates and the error bar the standard deviation.
    Pcr Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9768 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr master mix/product/Thermo Fisher
    Average 99 stars, based on 9768 article reviews
    Price from $9.99 to $1999.99
    pcr master mix - by Bioz Stars, 2020-07
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    99
    Thermo Fisher fast universal pcr master mix
    Effects of SPIB knock-down on resistant cells. a Conformation of partial silencing of SPIB on gene level. The relative mRNA expression of SPIB was assessed in the cells using <t>TaqMan</t> probe based <t>RT-PCR</t> and revealed a knock of gene expression with 50% compared to un-knocked control cells. The data are normalised to the S18 reference gene. b Protein levels of SPIB measured with western blot 48 h after transfection with siRNA. GAPDH was used as loading control. Representative figure of three biological replicates. c Normalised proliferation for Z138 cells grown in cytarabine containing medium, measured by incorporation of [methyl-14C]-thymidine 72 h after knock of SPIB using siRNA. Each data point represents a mean value of triplicates and error bars show SD. * = p
    Fast Universal Pcr Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 505 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fast universal pcr master mix/product/Thermo Fisher
    Average 99 stars, based on 505 article reviews
    Price from $9.99 to $1999.99
    fast universal pcr master mix - by Bioz Stars, 2020-07
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    Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Journal: Scientific Reports

    Article Title: Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

    doi: 10.1038/s41598-018-25299-7

    Figure Lengend Snippet: Results obtained in cross-reactivity tests performed with DNA isolates from 23 animal species with 5 commercial master mixes. ( A ) QuantiTect® Multiplex PCR NoROX Master Mix (Qiagen), ( B ) TaqMan® Universal PCR Master Mix (Applied Biosystems), ( C ) GoTaq® Probe qPCR Master Mix (Promega), ( D ) PerfeCTa® qPCR ToughMix TM , Low ROX TM (Quanta Biosciences) and E) Takyon TM No Rox Probe MasterMix dTTP Blue (Eurogentec).

    Article Snippet: The TaqMan® Universal PCR Master Mix (Applied Biosystems) led to a higher Ct value for sika deer (Ct = 26.74) than the other four master mixes (Ct ± SD = 25.11 ± 0.45), the ΔCt value between sika deer and the cross-reacting species was ≥12.06 (Fig. ).

    Techniques: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Estimation of linear range of phage particles by phage PCR. (a) Real-time PCR amplification of 10-fold serial dilutions of phage particles in water. Five μl of each preparation was mixed with 15 μl of PCR pre mix containing primers specific to the arabinose promoter of the phagemid vector and the 5’-FAM probe. (b) Standard curve of the phage PCR obtained by plotting the threshold Ct value of each dilution against the log number of phage particles added to the PCR pre mix. Each data point refers to an average of two replicates (c) Titration of 3-PBA phage particles forming the antibody-alalyte-phage complex in the PHAIA plate. The phage particles were recovered from PHAIA wells incubated with 0, 1, 5, and 25 ng/ml of 3-PBA. Each column represents the mean value of three replicates and the error bar the standard deviation.

    Journal: Analytical chemistry

    Article Title: Noncompetitive Phage Anti-Immunocomplex Real-Time PCR (PHAIA-PCR) for Sensitive Detection of Small Molecules

    doi: 10.1021/ac102353z

    Figure Lengend Snippet: Estimation of linear range of phage particles by phage PCR. (a) Real-time PCR amplification of 10-fold serial dilutions of phage particles in water. Five μl of each preparation was mixed with 15 μl of PCR pre mix containing primers specific to the arabinose promoter of the phagemid vector and the 5’-FAM probe. (b) Standard curve of the phage PCR obtained by plotting the threshold Ct value of each dilution against the log number of phage particles added to the PCR pre mix. Each data point refers to an average of two replicates (c) Titration of 3-PBA phage particles forming the antibody-alalyte-phage complex in the PHAIA plate. The phage particles were recovered from PHAIA wells incubated with 0, 1, 5, and 25 ng/ml of 3-PBA. Each column represents the mean value of three replicates and the error bar the standard deviation.

    Article Snippet: TaqMan probes (5’-FAM and 5’-VIC), 7500 Fast RT-PCR system, and PCR master mix (TaqMan® Universal PCR Master Mix (2X), No Amperase® UNG) were obtained from Applied Biosystems (Carlsbad, CA).

    Techniques: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Amplification, Plasmid Preparation, Titration, Incubation, Standard Deviation

    PHAIA-PCR and conventional PHAIA for 3-PBA and molinate. Five μl of phage particles eluted after incubation at various concentrations of analytes were mixed with 15 μl of PCR pre mix containing primers and 5’-FAM probe designed for universal amplification. Assay conditions of the PHAIA-PCR for each analyte are the same as the PHAIAs. Each value represents the mean value of three replicates (a) Amplification of 3-PBA phage. (b) Dose-response curves for 3-PBA. (c) Amplification of molinate phage. (d) Dose-response curves for molinate.

    Journal: Analytical chemistry

    Article Title: Noncompetitive Phage Anti-Immunocomplex Real-Time PCR (PHAIA-PCR) for Sensitive Detection of Small Molecules

    doi: 10.1021/ac102353z

    Figure Lengend Snippet: PHAIA-PCR and conventional PHAIA for 3-PBA and molinate. Five μl of phage particles eluted after incubation at various concentrations of analytes were mixed with 15 μl of PCR pre mix containing primers and 5’-FAM probe designed for universal amplification. Assay conditions of the PHAIA-PCR for each analyte are the same as the PHAIAs. Each value represents the mean value of three replicates (a) Amplification of 3-PBA phage. (b) Dose-response curves for 3-PBA. (c) Amplification of molinate phage. (d) Dose-response curves for molinate.

    Article Snippet: TaqMan probes (5’-FAM and 5’-VIC), 7500 Fast RT-PCR system, and PCR master mix (TaqMan® Universal PCR Master Mix (2X), No Amperase® UNG) were obtained from Applied Biosystems (Carlsbad, CA).

    Techniques: Polymerase Chain Reaction, Incubation, Amplification

    PHAIA-PCR using the 3-PBA peptide specific probe. Primers and the 5’-VIC probe designed for specific amplification of the DNA sequence encoding the anti 3-PBA/PAb 294 immunocomplex were used for 3-PBA (A) and molinate (B) PHAIA-PCR amplification. The insert in figure A plots dose-response curve as the Ct threshold values versus the 3-PBA concentration, each point represents the mean value of three replicates.

    Journal: Analytical chemistry

    Article Title: Noncompetitive Phage Anti-Immunocomplex Real-Time PCR (PHAIA-PCR) for Sensitive Detection of Small Molecules

    doi: 10.1021/ac102353z

    Figure Lengend Snippet: PHAIA-PCR using the 3-PBA peptide specific probe. Primers and the 5’-VIC probe designed for specific amplification of the DNA sequence encoding the anti 3-PBA/PAb 294 immunocomplex were used for 3-PBA (A) and molinate (B) PHAIA-PCR amplification. The insert in figure A plots dose-response curve as the Ct threshold values versus the 3-PBA concentration, each point represents the mean value of three replicates.

    Article Snippet: TaqMan probes (5’-FAM and 5’-VIC), 7500 Fast RT-PCR system, and PCR master mix (TaqMan® Universal PCR Master Mix (2X), No Amperase® UNG) were obtained from Applied Biosystems (Carlsbad, CA).

    Techniques: Polymerase Chain Reaction, Amplification, Sequencing, Concentration Assay

    The microRNA (miR)-96/182/183 cluster is upregulated in the livers of colesevelam-treated Zucker diabetic fatty (ZDF) rats. A : volcano plot depicting significantly altered miRNAs between colesevelam (Col) and vehicle-treated ZDF rat livers ( left ) and expression (reads per million total reads) of the miR-96/182/183 cluster ( left ); n = 6. B–D : liver expression of the miR-96/182/183 cluster by real-time PCR; n = 9–12. E : liver gene (mRNA) expression changes of Srebf2 and its target genes Hmgcr , Ldlr , and Sqle ; n = 8–12. For sequencing data, unpaired t -tests were used. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used; n.d., not detectable.

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: The microRNA (miR)-96/182/183 cluster is upregulated in the livers of colesevelam-treated Zucker diabetic fatty (ZDF) rats. A : volcano plot depicting significantly altered miRNAs between colesevelam (Col) and vehicle-treated ZDF rat livers ( left ) and expression (reads per million total reads) of the miR-96/182/183 cluster ( left ); n = 6. B–D : liver expression of the miR-96/182/183 cluster by real-time PCR; n = 9–12. E : liver gene (mRNA) expression changes of Srebf2 and its target genes Hmgcr , Ldlr , and Sqle ; n = 8–12. For sequencing data, unpaired t -tests were used. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used; n.d., not detectable.

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Sequencing, MANN-WHITNEY

    Mediator complex subunit 1 (Med1) is regulated by microRNA (miR)-96/182/183 in mice. A : expression of Med1 by real-time PCR in mouse primary hepatocytes transfected with 50 nM of Med1 or scramble siRNA; n = 3 B : Western blot of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with Med1 or scramble siRNA. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. A.U., arbitrary units. C : hepatic Med1 mRNA levels in db/db mice treated with vehicle or 2% colesevelam (Col)-supplemented diet and PBS or locked-nucleic acid (LNA)-182-5p; real-time PCR; n = 8–9. D : hepatic Med1 and β-actin (loading control) protein levels from 3 representative liver protein samples for Chow + PBS, Col + PBS, and Col + LNA-182. Western blotting. Ratio of Med1/β-actin densitometry is indicated between the blots. E : densitometry quantification of Med1 protein levels normalized to β-actin; n = 8–9. F : expression of miR-96-5p, miR-182-5p, and miR-183-5p in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, miR-183-5p mimics individually or in combination; real-time PCR; n = 3. G : Med1 mRNA levels in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 3. H : protein levels of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with mock or 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. For comparisons between 2 groups, Students’ t- tests were used, and for more than 2 groups, Kruskal-Wallis one-way ANOVA with Dunn’s posttest was used (α = 0.05) or one-way ANOVA with Bonferonni’s posttest for comparison to mock group only was used (α = 0.05).

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: Mediator complex subunit 1 (Med1) is regulated by microRNA (miR)-96/182/183 in mice. A : expression of Med1 by real-time PCR in mouse primary hepatocytes transfected with 50 nM of Med1 or scramble siRNA; n = 3 B : Western blot of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with Med1 or scramble siRNA. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. A.U., arbitrary units. C : hepatic Med1 mRNA levels in db/db mice treated with vehicle or 2% colesevelam (Col)-supplemented diet and PBS or locked-nucleic acid (LNA)-182-5p; real-time PCR; n = 8–9. D : hepatic Med1 and β-actin (loading control) protein levels from 3 representative liver protein samples for Chow + PBS, Col + PBS, and Col + LNA-182. Western blotting. Ratio of Med1/β-actin densitometry is indicated between the blots. E : densitometry quantification of Med1 protein levels normalized to β-actin; n = 8–9. F : expression of miR-96-5p, miR-182-5p, and miR-183-5p in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, miR-183-5p mimics individually or in combination; real-time PCR; n = 3. G : Med1 mRNA levels in mouse primary hepatocytes transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 3. H : protein levels of Med1 and β-actin (loading control) from protein samples of primary hepatocytes transfected with mock or 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 3. For comparisons between 2 groups, Students’ t- tests were used, and for more than 2 groups, Kruskal-Wallis one-way ANOVA with Dunn’s posttest was used (α = 0.05) or one-way ANOVA with Bonferonni’s posttest for comparison to mock group only was used (α = 0.05).

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

    Techniques: Mouse Assay, Expressing, Real-time Polymerase Chain Reaction, Transfection, Western Blot

    Mediator complex subunit 1 (MED1) is a direct target of microRNA (miR)-182-5p, miR-183-5p, and miR-96-5p in humans. A : schematic of human MED1 mRNA and the 3 putative miR-182/183/96 target sites in the 3′-untranslated region (3′-UTR). B : predicted MED1 3′-UTR target sites. Bases highlighted in dark gray represent mutations for gene reporter (luciferase) assays. C : normalized luciferase activity in HEK293 cells after dual transfection of miR-96/182/183 mimics and gene (luciferase) reporters harboring putative target sites for miR-96-5p, miR-182-5p, and/or miR-183-5p; n = 4. D : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. E : MED1 mRNA levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. F : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with mock or 50 nM locked-nucleic acids (LNAs) against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. G : MED1 mRNA levels in Huh7 cells transfected mock or 50 nM LNAs against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. H : protein levels of Med1 and β-actin (loading control) from protein lysates of Huh7 cells transfected with mock or 50 nM miR-96, miR-182, and miR-183 LNAs. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 6. A.U. arbitrary units. For comparisons between more than 2 groups to mock only, one-way ANOVA with Bonferonni’s posttest was used, α = 0.05. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used.

    Journal: American Journal of Physiology - Gastrointestinal and Liver Physiology

    Article Title: Liver and Biliary Tract Physiology/Pathophysiology: Intestinal bile acid sequestration improves glucose control by stimulating hepatic miR-182-5p in type 2 diabetes

    doi: 10.1152/ajpgi.00238.2018

    Figure Lengend Snippet: Mediator complex subunit 1 (MED1) is a direct target of microRNA (miR)-182-5p, miR-183-5p, and miR-96-5p in humans. A : schematic of human MED1 mRNA and the 3 putative miR-182/183/96 target sites in the 3′-untranslated region (3′-UTR). B : predicted MED1 3′-UTR target sites. Bases highlighted in dark gray represent mutations for gene reporter (luciferase) assays. C : normalized luciferase activity in HEK293 cells after dual transfection of miR-96/182/183 mimics and gene (luciferase) reporters harboring putative target sites for miR-96-5p, miR-182-5p, and/or miR-183-5p; n = 4. D : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. E : MED1 mRNA levels in Huh7 cells transfected with 50 nM miR-96-5p, miR-182-5p, and miR-183-5p mimics individually or in combination; real-time PCR; n = 6. F : miR-96-5p, miR-182-5p, and miR-183-5p levels in Huh7 cells transfected with mock or 50 nM locked-nucleic acids (LNAs) against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. G : MED1 mRNA levels in Huh7 cells transfected mock or 50 nM LNAs against miR-182-5p and/or miR-183-5p; real-time PCR; n = 6. H : protein levels of Med1 and β-actin (loading control) from protein lysates of Huh7 cells transfected with mock or 50 nM miR-96, miR-182, and miR-183 LNAs. Ratio of Med1/β-actin densitometry is indicated between the blots and graphed on the right ; n = 6. A.U. arbitrary units. For comparisons between more than 2 groups to mock only, one-way ANOVA with Bonferonni’s posttest was used, α = 0.05. For comparisons between 2 groups, Mann-Whitney nonparametric tests were used.

    Article Snippet: Real-time PCR was completed with Universal PCR Master Mix and TaqMan mRNA and miRNA assays (ThermoFisher).

    Techniques: Luciferase, Activity Assay, Transfection, Real-time Polymerase Chain Reaction, MANN-WHITNEY

    TaqMan genotyping assays discriminate seven SNPs differentiating BoHV-1.1 and BoHV-1.2 genomes. (A) Organization of the BoHV-1 genome including two unique sequences, a long one (UL) and a short one (US). The latter is flanked by two repeated and inverted sequences (IR, internal repeat; TR, terminal repeat). Shown are the localizations of the seven point mutations detected in seven BoHV-1 genes that are targeted by TaqMan genotyping assays. The nucleotides indicate the allelic version discriminating BoHV-1.1 (in boldface type) and BoHV-1.2 at each position. (B) Endpoint reading of the fluorescence generated during PCR amplification of seven target genes discriminating BoHV-1.1 (▪) and BoHV-1.2 (□). BoHV-1.1 DNA hybridized with the VIC-labeled probes, giving rise to an intense fluorescence along the x axis during amplification. BoHV-1.2 alleles hybridized with the FAM-labeled probes, resulting in a high fluorescence signal along the y axis. Different ratios of BoHV-1.1 and -1.2 DNA (1/10, 1/1, and 10/1) were mixed together and submitted to the analysis; these samples (▵) were hybridized with both the FAM- and VIC-labeled probes, resulting in increased fluorescence signals along both axes. Dot plot data were generated from endpoint readings of the fluorescence recorded after TaqMan PCR assays were performed on total DNA quantities ranging from 1 to 20 ng.

    Journal: Journal of Virology

    Article Title: Coinfection with Two Closely Related Alphaherpesviruses Results in a Highly Diversified Recombination Mosaic Displaying Negative Genetic Interference ▿

    doi: 10.1128/JVI.02474-08

    Figure Lengend Snippet: TaqMan genotyping assays discriminate seven SNPs differentiating BoHV-1.1 and BoHV-1.2 genomes. (A) Organization of the BoHV-1 genome including two unique sequences, a long one (UL) and a short one (US). The latter is flanked by two repeated and inverted sequences (IR, internal repeat; TR, terminal repeat). Shown are the localizations of the seven point mutations detected in seven BoHV-1 genes that are targeted by TaqMan genotyping assays. The nucleotides indicate the allelic version discriminating BoHV-1.1 (in boldface type) and BoHV-1.2 at each position. (B) Endpoint reading of the fluorescence generated during PCR amplification of seven target genes discriminating BoHV-1.1 (▪) and BoHV-1.2 (□). BoHV-1.1 DNA hybridized with the VIC-labeled probes, giving rise to an intense fluorescence along the x axis during amplification. BoHV-1.2 alleles hybridized with the FAM-labeled probes, resulting in a high fluorescence signal along the y axis. Different ratios of BoHV-1.1 and -1.2 DNA (1/10, 1/1, and 10/1) were mixed together and submitted to the analysis; these samples (▵) were hybridized with both the FAM- and VIC-labeled probes, resulting in increased fluorescence signals along both axes. Dot plot data were generated from endpoint readings of the fluorescence recorded after TaqMan PCR assays were performed on total DNA quantities ranging from 1 to 20 ng.

    Article Snippet: PCRs were carried out using 10 ng of dried cellular/viral DNA in a final volume of 5 μl composed of 2.5 μl of TaqMan PCR master mix (Applied Biosystems), 0.125 μl of one SNP genotyping assay mixture containing the two primers and the two probes designed for one target SNP, and 2.375 μl of nuclease-free water.

    Techniques: Fluorescence, Generated, Polymerase Chain Reaction, Amplification, Labeling

    Amplification of Epstein-Barr virus (EBV) from DNA isolated from breast cancer and blood specimens. Real time PCR using minor groove binding (MGB)-TaqMan technology was used to quantify the viral load contained in the samples. Internal repeat region (IR)1 target sequences showed that this probe amplified its respective target over a broad range and detected low levels (2.3 EBV genomes per reaction; unpublished observation). (a) A characteristic amplification plot showing the change in fluorescence (ΔRn) as a function of amplification cycle. The horizontal red line indicates the fluorescence at 10× the standard deviation of the control. The upper left arrow indicates the fluorescence detected from Daudi, an EBV-associated endemic Burkitt lymphoma. The lower arrow indicates the fluorescence of a negative control (water). The amplification, in triplicate, of the DNA from each of the patient tumor samples is indicated. (b) The standard was constructed to contain from 2 to 200,000 copies of EBV genome. The graph shows the linear regression of the Cts (the PCR cycle number when the amplification fluorescence value reaches and exceeds the predetermined background threshold value) using each of the standards. This characteristic standard line had an r 2 = 0.995 with a slope of -3.2.

    Journal: Breast Cancer Research

    Article Title: Analysis of Epstein-Barr virus reservoirs in paired blood and breast cancer primary biopsy specimens by real time PCR

    doi: 10.1186/bcr1627

    Figure Lengend Snippet: Amplification of Epstein-Barr virus (EBV) from DNA isolated from breast cancer and blood specimens. Real time PCR using minor groove binding (MGB)-TaqMan technology was used to quantify the viral load contained in the samples. Internal repeat region (IR)1 target sequences showed that this probe amplified its respective target over a broad range and detected low levels (2.3 EBV genomes per reaction; unpublished observation). (a) A characteristic amplification plot showing the change in fluorescence (ΔRn) as a function of amplification cycle. The horizontal red line indicates the fluorescence at 10× the standard deviation of the control. The upper left arrow indicates the fluorescence detected from Daudi, an EBV-associated endemic Burkitt lymphoma. The lower arrow indicates the fluorescence of a negative control (water). The amplification, in triplicate, of the DNA from each of the patient tumor samples is indicated. (b) The standard was constructed to contain from 2 to 200,000 copies of EBV genome. The graph shows the linear regression of the Cts (the PCR cycle number when the amplification fluorescence value reaches and exceeds the predetermined background threshold value) using each of the standards. This characteristic standard line had an r 2 = 0.995 with a slope of -3.2.

    Article Snippet: Amplification was performed in a total of 20 μl containing 2× Universal TaqMan PCR master mix (Applied Biosystems, Foster City, CA, USA) 900 nM of BAMHIW (forward primer, 5'-CCC AAC ACT CCA CCA CAC C-3'; reverse primers, 5'-TCT TAG GAG CTG TCC GAG GG-3'), 250 nM of Probe LIR-1MGB2 (FAM-ACACTACACACACCCACC-MGBNFQ) and 1.75 μl of water.

    Techniques: Amplification, Isolation, Real-time Polymerase Chain Reaction, Binding Assay, Fluorescence, Standard Deviation, Negative Control, Construct, Polymerase Chain Reaction

    CKS1B and CKS2 expression is higher in diagnostic bone marrow samples from patients carrying MLL -translocations compared to PBMCs from healthy controls. RNA extracted from human umbilical cord blood CD34 + cells, PBMCs from healthy donors, and leukaemic patient samples, were assessed for (A) CKS1B and (B) CKS2 expression by TaqMan quantitative PCR. Three independent control genes were used ( ABL , GUS , B2M ) to measure relative RNA abundance. Values are represented as relative gene expression versus GUS control. Each point represents one patient. Median bars with standard deviation are presented for each set of samples. A Student's t -test was used to assess significance, and * indicates significance versus CD34 + cells, and § indicates significance versus PBMCs.

    Journal: Biochimica et Biophysica Acta

    Article Title: The Cks1/Cks2 axis fine-tunes Mll1 expression and is crucial for MLL-rearranged leukaemia cell viability

    doi: 10.1016/j.bbamcr.2017.09.009

    Figure Lengend Snippet: CKS1B and CKS2 expression is higher in diagnostic bone marrow samples from patients carrying MLL -translocations compared to PBMCs from healthy controls. RNA extracted from human umbilical cord blood CD34 + cells, PBMCs from healthy donors, and leukaemic patient samples, were assessed for (A) CKS1B and (B) CKS2 expression by TaqMan quantitative PCR. Three independent control genes were used ( ABL , GUS , B2M ) to measure relative RNA abundance. Values are represented as relative gene expression versus GUS control. Each point represents one patient. Median bars with standard deviation are presented for each set of samples. A Student's t -test was used to assess significance, and * indicates significance versus CD34 + cells, and § indicates significance versus PBMCs.

    Article Snippet: Quantitative PCR analyses were carried out using either the Quantitect SYBR Green RT-PCR kit (MEFs – Qiagen) or the TaqMan Universal PCR Master Mix kit (MLL -translocation cell lines – ThermoScientific).

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

    The expression of GDNF mRNA is increased in iris from dTC-treated embryos at E17. The relative expression of (A) GDNF, (B) CNTF, or (C) BDNF mRNA in E15 and E17 iris tissue after treatment with saline (light bars) or 2 mg/day of dTC (dark bars) from E8–E16 was quantified with real-time PCR using Taqman probes. The mRNA expression was normalized to chicken ribosomal protein s17 (Chrps). Each bar represents the mean normalized arbitrary units (AU) of the indicated number of irises, which were separately extracted for total RNA. Each iris represents a different animal. Each qPCR run was performed using duplicate samples of template from each iris. The error bars represent standard deviation. Statistical analysis was done using a two way ANOVA with a Bonferroni post test (* p

    Journal: Developmental neurobiology

    Article Title: Differential Effects of RET and TRKB on Axonal Branching and Survival of Parasympathetic Neurons

    doi: 10.1002/dneu.22036

    Figure Lengend Snippet: The expression of GDNF mRNA is increased in iris from dTC-treated embryos at E17. The relative expression of (A) GDNF, (B) CNTF, or (C) BDNF mRNA in E15 and E17 iris tissue after treatment with saline (light bars) or 2 mg/day of dTC (dark bars) from E8–E16 was quantified with real-time PCR using Taqman probes. The mRNA expression was normalized to chicken ribosomal protein s17 (Chrps). Each bar represents the mean normalized arbitrary units (AU) of the indicated number of irises, which were separately extracted for total RNA. Each iris represents a different animal. Each qPCR run was performed using duplicate samples of template from each iris. The error bars represent standard deviation. Statistical analysis was done using a two way ANOVA with a Bonferroni post test (* p

    Article Snippet: Real-time PCR primers and probes were designed as described in Taqman Universal PCR Master Mix protocol (Applied Biosystems, Foster City, CA; ).

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

    PCR amplification using TaqMan probe chemistry. After probe and primers bind to the template ( Step 1 ), Taq polymerase initiates synthesis, displaces and cleaves the probe ( Step 2 and 3 ), which allows fluorescence to be emitted. Polymerization is completed after one cycle of PCR amplification ( Step 4 ).

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Real-Time PCR Analysis of HIV-1 Replication Post-entry Events

    doi: 10.1007/978-1-59745-170-3_5

    Figure Lengend Snippet: PCR amplification using TaqMan probe chemistry. After probe and primers bind to the template ( Step 1 ), Taq polymerase initiates synthesis, displaces and cleaves the probe ( Step 2 and 3 ), which allows fluorescence to be emitted. Polymerization is completed after one cycle of PCR amplification ( Step 4 ).

    Article Snippet: There are commercially available PCRmaster mixes, e.g., Taq-Man Universal PCR Master Mix (PE-Applied Biosystems), that contain all the PCR reagents in a single tube except for the primers, probe and DNA.

    Techniques: Polymerase Chain Reaction, Amplification, Fluorescence

    SNCA mRNA and α-Synuclein Protein Levels in the MD NPC Lines Carrying the gRNA-dCas9-DNMT3A Transgenes (A) Levels of SNCA mRNA were assessed using qRT-PCR. The SNCA mRNA levels in the different lines were measured by TaqMan-based gene expression assays and calculated relative to the geometric mean of GAPDH mRNA and PPIA mRNA reference controls using the 2 −ΔΔCt method. Each bar represents the mean ± SEM of four biological and two technical replicates for a particular MD NPC line. The calibrator was a particular RNA sample of the control MD NPCs that was included in all runs. (B and C) The levels of α-synuclein protein were semi-quantified by western blot using the α-synuclein rabbit monoclonal antibody normalized to β-actin mAb. (B) The two lanes represent the analysis performed using the samples of the following MD NPC lines: gRNA4-dCas9-DNMT3A and dCas9-DNMT3A no-gRNA. (C) Quantification of the α-synuclein protein signals for each MD NPC line using ImageJ. Bars represents the intensity of the bands ± SEM of two biological and technical repeats. (D–G) Representative immunocytochemistry images for the α-synuclein signal (D and F) and the α-synuclein and Nestin double-staining signals (E and G) of the MD NPC lines. Scale bars, 10 μm. (H) Quantification of the α-synuclein protein signal in the MD NPC line carrying the gRNA4-dCas9-DNMT3A vector and the control line with the no-gRNA vector. 50 cells were imaged in two independent experiments. Bars represent the means ± SEM of the intensity of α-synuclein staining in a total of 100 cells. *p

    Journal: Molecular Therapy

    Article Title: Downregulation of SNCA Expression by Targeted Editing of DNA Methylation: A Potential Strategy for Precision Therapy in PD

    doi: 10.1016/j.ymthe.2018.08.019

    Figure Lengend Snippet: SNCA mRNA and α-Synuclein Protein Levels in the MD NPC Lines Carrying the gRNA-dCas9-DNMT3A Transgenes (A) Levels of SNCA mRNA were assessed using qRT-PCR. The SNCA mRNA levels in the different lines were measured by TaqMan-based gene expression assays and calculated relative to the geometric mean of GAPDH mRNA and PPIA mRNA reference controls using the 2 −ΔΔCt method. Each bar represents the mean ± SEM of four biological and two technical replicates for a particular MD NPC line. The calibrator was a particular RNA sample of the control MD NPCs that was included in all runs. (B and C) The levels of α-synuclein protein were semi-quantified by western blot using the α-synuclein rabbit monoclonal antibody normalized to β-actin mAb. (B) The two lanes represent the analysis performed using the samples of the following MD NPC lines: gRNA4-dCas9-DNMT3A and dCas9-DNMT3A no-gRNA. (C) Quantification of the α-synuclein protein signals for each MD NPC line using ImageJ. Bars represents the intensity of the bands ± SEM of two biological and technical repeats. (D–G) Representative immunocytochemistry images for the α-synuclein signal (D and F) and the α-synuclein and Nestin double-staining signals (E and G) of the MD NPC lines. Scale bars, 10 μm. (H) Quantification of the α-synuclein protein signal in the MD NPC line carrying the gRNA4-dCas9-DNMT3A vector and the control line with the no-gRNA vector. 50 cells were imaged in two independent experiments. Bars represent the means ± SEM of the intensity of α-synuclein staining in a total of 100 cells. *p

    Article Snippet: Each cDNA (20 ng) was amplified in duplicate in at least two independent runs for two independent experiments (overall ≥8 repeats), using TaqMan Universal PCR master mix reagent (Applied Biosystems) and the following conditions: 2 min at 50°C, 10 min at 95°C, and 40 cycles of 15 s at 95°C and 1 min at 60°C.

    Techniques: Quantitative RT-PCR, Expressing, Western Blot, Immunocytochemistry, Double Staining, Plasmid Preparation, Staining

    Characterization of the Stably Transduced SNCA-Tri MD NPCs Representative immunocytochemistry images of the SNCA-Tri MD NPCs carrying the gRNA-dCas9-DNMT3A transgene. (A–J) MD NPCs showed the expression of Nestin (A–E) and FoxA2 (F–J) with no gRNA (A and F), gRNA1 (B and G), gRNA2 (C and H), gRNA3 (D and I), or gRNA4 (E and J). Scale bars, 10 μm. (K and L) MD NPC markers were evaluated using real-time qRT-PCR for (K) Nestin and (L) FoxA2. The levels of mRNAs were measured by TaqMan expression assays and calculated relative to the geometric mean of GAPDH mRNA and PPIA mRNA reference controls using the 2 −ΔΔCT method. Each column represents the mean of two biological and technical replicates. The error bars represent the SEM.

    Journal: Molecular Therapy

    Article Title: Downregulation of SNCA Expression by Targeted Editing of DNA Methylation: A Potential Strategy for Precision Therapy in PD

    doi: 10.1016/j.ymthe.2018.08.019

    Figure Lengend Snippet: Characterization of the Stably Transduced SNCA-Tri MD NPCs Representative immunocytochemistry images of the SNCA-Tri MD NPCs carrying the gRNA-dCas9-DNMT3A transgene. (A–J) MD NPCs showed the expression of Nestin (A–E) and FoxA2 (F–J) with no gRNA (A and F), gRNA1 (B and G), gRNA2 (C and H), gRNA3 (D and I), or gRNA4 (E and J). Scale bars, 10 μm. (K and L) MD NPC markers were evaluated using real-time qRT-PCR for (K) Nestin and (L) FoxA2. The levels of mRNAs were measured by TaqMan expression assays and calculated relative to the geometric mean of GAPDH mRNA and PPIA mRNA reference controls using the 2 −ΔΔCT method. Each column represents the mean of two biological and technical replicates. The error bars represent the SEM.

    Article Snippet: Each cDNA (20 ng) was amplified in duplicate in at least two independent runs for two independent experiments (overall ≥8 repeats), using TaqMan Universal PCR master mix reagent (Applied Biosystems) and the following conditions: 2 min at 50°C, 10 min at 95°C, and 40 cycles of 15 s at 95°C and 1 min at 60°C.

    Techniques: Stable Transfection, Immunocytochemistry, Expressing, Quantitative RT-PCR

    miRNA expression pattern in response to Aβ time course in murine primary hippocampal neurons assessed by real-time PCR using TaqMan assays. Independent primary neuronal preparations treated with Aβ42 for 1, 6 or 15 hours were assayed for miRNA expression relative to untreated controls. T-test P-value significance: ***P

    Journal: PLoS ONE

    Article Title: Neuronal MicroRNA Deregulation in Response to Alzheimer's Disease Amyloid-?

    doi: 10.1371/journal.pone.0011070

    Figure Lengend Snippet: miRNA expression pattern in response to Aβ time course in murine primary hippocampal neurons assessed by real-time PCR using TaqMan assays. Independent primary neuronal preparations treated with Aβ42 for 1, 6 or 15 hours were assayed for miRNA expression relative to untreated controls. T-test P-value significance: ***P

    Article Snippet: 10 ng of total RNA was used in the RT reaction and the transcribed cDNA was then used for subsequent PCR amplification using TaqMan 2X Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems) as described by the manufacturer.

    Techniques: Expressing, Real-time Polymerase Chain Reaction

    In vivo analysis of the Aβ plaque-forming APP23 mouse model. A . In situ hybridization showing APP expression pattern in brains of three month-old APP23 versus wild-type mice. Note the high expression of the transgene in cortex and hippocampus. B . Immunohistochemistry with the 6E10 antibody showing high levels of Aβ in the hippocampus of three month-old APP23 mice compared to littermate controls. Scale bar = 500 µm. C–E . miRNA expression in hippocampus of two- ( C .), seven- ( D .) and thirteen- ( E .) month-old APP23 mice compared to wild-type littermate controls (n = 4) represented as fold change (FC) as determined using real-time PCR with TaqMan assays. Down-regulated miRNAs have been highlighted in green and up-regulated ones in red. Reactions were normalized to snoRNA135 and P-value significance was calculated using the Students T-test: P-value = *

    Journal: PLoS ONE

    Article Title: Neuronal MicroRNA Deregulation in Response to Alzheimer's Disease Amyloid-?

    doi: 10.1371/journal.pone.0011070

    Figure Lengend Snippet: In vivo analysis of the Aβ plaque-forming APP23 mouse model. A . In situ hybridization showing APP expression pattern in brains of three month-old APP23 versus wild-type mice. Note the high expression of the transgene in cortex and hippocampus. B . Immunohistochemistry with the 6E10 antibody showing high levels of Aβ in the hippocampus of three month-old APP23 mice compared to littermate controls. Scale bar = 500 µm. C–E . miRNA expression in hippocampus of two- ( C .), seven- ( D .) and thirteen- ( E .) month-old APP23 mice compared to wild-type littermate controls (n = 4) represented as fold change (FC) as determined using real-time PCR with TaqMan assays. Down-regulated miRNAs have been highlighted in green and up-regulated ones in red. Reactions were normalized to snoRNA135 and P-value significance was calculated using the Students T-test: P-value = *

    Article Snippet: 10 ng of total RNA was used in the RT reaction and the transcribed cDNA was then used for subsequent PCR amplification using TaqMan 2X Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems) as described by the manufacturer.

    Techniques: In Vivo, In Situ Hybridization, Expressing, Mouse Assay, Immunohistochemistry, Real-time Polymerase Chain Reaction

    Effects of SPIB knock-down on resistant cells. a Conformation of partial silencing of SPIB on gene level. The relative mRNA expression of SPIB was assessed in the cells using TaqMan probe based RT-PCR and revealed a knock of gene expression with 50% compared to un-knocked control cells. The data are normalised to the S18 reference gene. b Protein levels of SPIB measured with western blot 48 h after transfection with siRNA. GAPDH was used as loading control. Representative figure of three biological replicates. c Normalised proliferation for Z138 cells grown in cytarabine containing medium, measured by incorporation of [methyl-14C]-thymidine 72 h after knock of SPIB using siRNA. Each data point represents a mean value of triplicates and error bars show SD. * = p

    Journal: BMC Cancer

    Article Title: Bortezomib prevents cytarabine resistance in MCL, which is characterized by down-regulation of dCK and up-regulation of SPIB resulting in high NF-κB activity

    doi: 10.1186/s12885-018-4346-1

    Figure Lengend Snippet: Effects of SPIB knock-down on resistant cells. a Conformation of partial silencing of SPIB on gene level. The relative mRNA expression of SPIB was assessed in the cells using TaqMan probe based RT-PCR and revealed a knock of gene expression with 50% compared to un-knocked control cells. The data are normalised to the S18 reference gene. b Protein levels of SPIB measured with western blot 48 h after transfection with siRNA. GAPDH was used as loading control. Representative figure of three biological replicates. c Normalised proliferation for Z138 cells grown in cytarabine containing medium, measured by incorporation of [methyl-14C]-thymidine 72 h after knock of SPIB using siRNA. Each data point represents a mean value of triplicates and error bars show SD. * = p

    Article Snippet: For confirmation of mRNA expression in different samples, TaqMan probe-based RT-PCR was performed, using TaqMan® Fast Universal PCR Master Mix (Applied Biosystem, Waltham, MA, USA) and the TaqMan assay Hs01040726_m1 (dCK, Applied Biosystem) and Hs00162150_m1 (SPIB, Applied Biosystem).

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Western Blot, Transfection

    Verification of dCK mRNA expression in gene microarray samples. The relative mRNA expression of dCK was assessed in the different Z138 subclones using TaqMan probe based RT-PCR and revealed down-regulation in both Z138-CytES and Z138-CytR cells compared to Z138-CytNS cells. The data are normalised to the S18 reference gene, and the reference sample, replicate A of the Z138-CytNS for each run. Bars represent relative quantity ± SEM of three technical replicates. * = p

    Journal: BMC Cancer

    Article Title: Bortezomib prevents cytarabine resistance in MCL, which is characterized by down-regulation of dCK and up-regulation of SPIB resulting in high NF-κB activity

    doi: 10.1186/s12885-018-4346-1

    Figure Lengend Snippet: Verification of dCK mRNA expression in gene microarray samples. The relative mRNA expression of dCK was assessed in the different Z138 subclones using TaqMan probe based RT-PCR and revealed down-regulation in both Z138-CytES and Z138-CytR cells compared to Z138-CytNS cells. The data are normalised to the S18 reference gene, and the reference sample, replicate A of the Z138-CytNS for each run. Bars represent relative quantity ± SEM of three technical replicates. * = p

    Article Snippet: For confirmation of mRNA expression in different samples, TaqMan probe-based RT-PCR was performed, using TaqMan® Fast Universal PCR Master Mix (Applied Biosystem, Waltham, MA, USA) and the TaqMan assay Hs01040726_m1 (dCK, Applied Biosystem) and Hs00162150_m1 (SPIB, Applied Biosystem).

    Techniques: Expressing, Microarray, Reverse Transcription Polymerase Chain Reaction