taqman universal pcr master mix  (Thermo Fisher)


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    Structured Review

    Thermo Fisher taqman universal pcr master mix
    LBH589 induces expression of GADD45G mRNA and enhances acetylation of histones at the GADD45G promoter in MOLT-4 and Reh cells. (A) Following treatment with 50 nM LBH589 for 24 hours, <t>TaqMan</t> real-time <t>PCR</t> was performed on MOLT-4 and Reh cells. The mRNA
    Taqman Universal Pcr Master Mix, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5061 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 5061 article reviews
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    Images

    1) Product Images from "The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells"

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells

    Journal:

    doi: 10.1182/blood-2007-10-117762

    LBH589 induces expression of GADD45G mRNA and enhances acetylation of histones at the GADD45G promoter in MOLT-4 and Reh cells. (A) Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on MOLT-4 and Reh cells. The mRNA
    Figure Legend Snippet: LBH589 induces expression of GADD45G mRNA and enhances acetylation of histones at the GADD45G promoter in MOLT-4 and Reh cells. (A) Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on MOLT-4 and Reh cells. The mRNA

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    LBH589 induces expression of GADD45G mRNA in cultured primary Ph − ALL cells. Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on the cDNA from 6 patient samples. The mRNA levels were normalized to levels of
    Figure Legend Snippet: LBH589 induces expression of GADD45G mRNA in cultured primary Ph − ALL cells. Following treatment with 50 nM LBH589 for 24 hours, TaqMan real-time PCR was performed on the cDNA from 6 patient samples. The mRNA levels were normalized to levels of

    Techniques Used: Expressing, Cell Culture, Real-time Polymerase Chain Reaction

    2) Product Images from "Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis"

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis

    Journal: The Journal of Pharmacology and Experimental Therapeutics

    doi: 10.1124/jpet.113.203653

    Changes in GABA A R subunit expression in the hippocampus CA1, CA3, and DG subfields over the ovarian cycle. (A–C) TaqMan RT-PCR analysis of GABA A R subunits mRNA expression in the hippocampus. (D and E) Western blot analysis of δ -subunit
    Figure Legend Snippet: Changes in GABA A R subunit expression in the hippocampus CA1, CA3, and DG subfields over the ovarian cycle. (A–C) TaqMan RT-PCR analysis of GABA A R subunits mRNA expression in the hippocampus. (D and E) Western blot analysis of δ -subunit

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

    3) Product Images from "LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation"

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation

    Journal:

    doi: 10.1128/AEM.71.5.2372-2380.2005

    Real-time quantitative RT-PCR analysis of gtfB , gtfC , and gtfD gene expression at different growth stages of S. mutans GS-5 and the luxS mutant. The relative quantities of each gtf cDNA from S. mutans GS-5 and the luxS mutant were assessed by TaqMan assays.
    Figure Legend Snippet: Real-time quantitative RT-PCR analysis of gtfB , gtfC , and gtfD gene expression at different growth stages of S. mutans GS-5 and the luxS mutant. The relative quantities of each gtf cDNA from S. mutans GS-5 and the luxS mutant were assessed by TaqMan assays.

    Techniques Used: Quantitative RT-PCR, Expressing, Mutagenesis

    4) Product Images from "Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia"

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia

    Journal: Genes, chromosomes & cancer

    doi: 10.1002/gcc.20654

    Expression of ZNF342 in AML Samples. TaqMan qRT-PCR analysis of ZNF342 confirming overexpression in MH500 and demonstrating a variable expression in additional leukemia samples, with no significant increase in ZNF342 expression in samples containing an
    Figure Legend Snippet: Expression of ZNF342 in AML Samples. TaqMan qRT-PCR analysis of ZNF342 confirming overexpression in MH500 and demonstrating a variable expression in additional leukemia samples, with no significant increase in ZNF342 expression in samples containing an

    Techniques Used: Expressing, Quantitative RT-PCR, Over Expression

    5) Product Images from "Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells by a paracrine mechanism"

    Article Title: Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells by a paracrine mechanism

    Journal:

    doi: 10.1182/blood-2007-09-113654

    HTLV-I Tax-transactivated IL-9 expression in Jurkat T cells . (A) IL-9 mRNA levels after Tax induction were detected by Taqman real-time PCR. The copy number of IL-9 mRNA was normalized by the copy number of hypoxanthine guanine phosphoribosyl transferase
    Figure Legend Snippet: HTLV-I Tax-transactivated IL-9 expression in Jurkat T cells . (A) IL-9 mRNA levels after Tax induction were detected by Taqman real-time PCR. The copy number of IL-9 mRNA was normalized by the copy number of hypoxanthine guanine phosphoribosyl transferase

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    6) Product Images from "Reconstruction of liver organoid using a bioreactor"

    Article Title: Reconstruction of liver organoid using a bioreactor

    Journal:

    doi: 10.3748/wjg.v12.i12.1881

    Comparison of expressions of CPS1, OTC, ASS, ASL, and ARG mRNA in FLC-5 incubated under different conditions as assessed by TaqMan 1-step RT-PCR. The mRNA expression of each enzyme in different conditions is relative to that in monolayer cultures. Mean
    Figure Legend Snippet: Comparison of expressions of CPS1, OTC, ASS, ASL, and ARG mRNA in FLC-5 incubated under different conditions as assessed by TaqMan 1-step RT-PCR. The mRNA expression of each enzyme in different conditions is relative to that in monolayer cultures. Mean

    Techniques Used: Incubation, Reverse Transcription Polymerase Chain Reaction, Expressing

    Related Articles

    Amplification:

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA). .. The amplification efficiency of MARRS and VDR were normalized using the endogenous control, GAPDH .

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: .. Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ). .. It was necessary to sequence a fragment of the cDNA containing part of exon 10 through intron 11 to synthesize a pair of primers adequate to carry out the real-time RT-PCR.

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: .. All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min. .. Relative expression levels for each miR were calculated based upon the expression of RNU66 and differences in gene expression were determined relative to normal breast tissues from reduction mammoplasties using the comparative Ct method described in the ABI Prism 7700 User Bulletin #2 (Applied Biosystems/Life Technologies).

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye. .. For each PCR, a mixture containing template cDNA, 1× Master Mix, 200 nM concentrations of each forward and reverse primer, and 250 nM TaqMan probe was applied to a 96-well MicroAmp optical reaction plate with optical caps (Applied Biosystems).

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ]. .. Amplification and detection were performed using an Applied Biosystems Prism 7900HT sequence detection system with SDS 2.2.1 software (Applied Biosystems) at the following conditions: 2 min at 50°C and 10 min at 95°C, then 45 cycles of 15 s at 95°C and 1 min at 60°C.

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR. .. A relative standard curve method (Applied Biosystems) was used to calculate the amplification difference in urea cycle-related enzymes between cocultured and control cells, and elongation factor 1 (EF1), for each primer set and between albumin, HNF-1, HNF-4, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH).

    Synthesized:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Single-stranded cDNA was then synthesized in a reaction mixture containing 1.25 U of MultiScribe reverse transcriptase/μl, 0.4 U of RNase inhibitor/μl, 500 mM concentrations of each deoxynucleoside triphosphate, a 200 mM concentration of antisense primer, 1× reverse transcription (RT) buffer, 5.5 mM MgCl2 (TaqMan reverse transcription reagents; Applied Biosystems), and 1.0 μg of total RNA from each phase of culture at 48°C for 30 min. To check for DNA contamination, purified total RNA without reverse transcriptase served as a negative control. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Construct:

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems). .. BAC RP11-815F2 constructs containing DNA fragments covering the tested regions were used as template controls for normalizing digestion, ligation and primer efficiency.

    SYBR Green Assay:

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: The QuantiTect SYBR Green RT-PCR kit (Qiagen, 204143) was used and the 25 μl reaction contained 1× QuantiTect SYBR Green RT-PCR master mix, 1.6 μM each primer, 0.25 μl QuantiTect RT Mix, and 100 ng template RNA. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Expressing:

    Article Title: PAHSAs enhance hepatic and systemic insulin sensitivity through direct and indirect mechanisms
    Article Snippet: .. Real-time PCRs for G6pc1 and Pck1 were performed on an ABI Prism 7900HT sequence detection system (Applied Biosystems) with TaqMan Universal PCR Master Mix and TaqMan gene expression assays (Applied Biosystems). .. Relative expression levels were determined using the ΔΔCt method.

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: Real Time PCR To examine MARRS and VDR mRNA expression, HL-60 and MV-4-11 cells were cultured in 24-well plates (2 × 105 cells per mL). .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA).

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells
    Article Snippet: TaqMan real-time PCR was carried out in MicroAmp optical 384-well reaction plates (Applied Biosystems) by an ABI Prism 7900HT Sequence Detection System (Applied Biosystems) using TaqMan Universal PCR Master Mix (Applied Biosystems) and following standard “TaqMan” procedures. .. For quantification, target gene expression was normalized by comparison with β- actin expression.

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: Paragraph title: Gene expression ... Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ).

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: Paragraph title: MicroRNA expression analysis ... All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min.

    Article Title: Cellular and molecular basis for stress-induced depression
    Article Snippet: Taqman Universal PCR Master Mix (Life Technologies, Foster City, CA, USA) was used for all analyses. .. Taqman gene expression assays (FAM) from Life Technologies were as follows: p11 (Mm00501457_m1) and Gapdh (Mm99999915_g1).

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: Levels of expression were compared between MH500, three additional AML samples, one normal bone marrow, and KG-1 and U937 cell lines. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis
    Article Snippet: The GABAA R subunit mRNA expression was determined by the TaqMan real-time PCR assay as described previously ( ). .. Real-time PCR was performed with TaqMan Universal PCR Master Mix (Applied Biosystems), which contained AmpliTaq Gold DNA polymerase, AmpErase, uracil-N-glycosylase (to prevent contamination from previous qPCR reactions), dNTPs with dUTP, and optimized buffer components.

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: .. TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR. .. A standard curve for serial dilution of 18S rRNAs was generated similarly.

    Real-time Polymerase Chain Reaction:

    Article Title: Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells by a paracrine mechanism
    Article Snippet: Paragraph title: Taqman real-time PCR ... The Taqman Universal PCR Master Mix, the IL-9 primer/probe, HTLV-I Tax primer/probe, and the HPRT1 primer/probe sets were purchased from Applied Biosystems (Foster City, CA).

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: Microfluidic dPCR Microfluidic dPCR experiments (MethyLight dPCR and RE digestion dPCR) were performed in accordance with the Minimum Information for Publication of Digital Quantitative PCR Experiments (digital MIQE) guidelines (Additional file ) using the Biomark system with 48 panel “qdPCRTM 37 K” integrated fluidic circuits (IFCs), Cat. No. 100–6152 (Fluidigm, South San Francisco, CA, USA). .. Assays were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion dPCR and 1 × Taqman Universal PCR mastermix (no Uracil-DNA Glycosylase), Cat no. 4324018 (Life Technologies) for MethyLight dPCR.

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA). .. The following protocol were used: 95 °C for 10 min, followed by 40 cycles of two step PCR, including denaturation at 95 °C for 15 s and annealing/extension at 60 °C for 1 min.

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells
    Article Snippet: .. TaqMan real-time PCR was carried out in MicroAmp optical 384-well reaction plates (Applied Biosystems) by an ABI Prism 7900HT Sequence Detection System (Applied Biosystems) using TaqMan Universal PCR Master Mix (Applied Biosystems) and following standard “TaqMan” procedures. .. For quantification, target gene expression was normalized by comparison with β- actin expression.

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: .. All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min. .. Relative expression levels for each miR were calculated based upon the expression of RNU66 and differences in gene expression were determined relative to normal breast tissues from reduction mammoplasties using the comparative Ct method described in the ABI Prism 7700 User Bulletin #2 (Applied Biosystems/Life Technologies).

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: .. Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems). ..

    Article Title: Cellular and molecular basis for stress-induced depression
    Article Snippet: Quantitative PCR was carried out using an Applied Biosystems 7900HT system (Foster City, CA, USA). .. Taqman Universal PCR Master Mix (Life Technologies, Foster City, CA, USA) was used for all analyses.

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Virus was measured by real-time PCR using influenza specific primers as previously described [ ]. cDNA synthesis was performed using both a specific primer (5′-TCTAACCGAGGTCGAAACGTA-3′) and random hexamers. .. Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ].

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis
    Article Snippet: .. Real-time PCR was performed with TaqMan Universal PCR Master Mix (Applied Biosystems), which contained AmpliTaq Gold DNA polymerase, AmpErase, uracil-N-glycosylase (to prevent contamination from previous qPCR reactions), dNTPs with dUTP, and optimized buffer components. .. Briefly, each sample was run in triplicate design and each 25- μ l reaction mixture consisted of 12.5- μ l of TaqMan Universal PCR Master mix, 400 nM primers, and 300 nM TaqMan probe for each targeted genes as described previously ( ).

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: .. Reactions were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion qPCR and 1 × Taqman Universal PCR mastermix without Uracil-DNA Glycosylase, Cat no. 4324018 (Life Technologies) for MethyLight qPCR in a final volume of 20 μL. .. All reactions also contained 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for primer and probe sequences and Additional file for details of assay performance) and 5 ng template DNA.

    Ligation:

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems). .. BAC RP11-815F2 constructs containing DNA fragments covering the tested regions were used as template controls for normalizing digestion, ligation and primer efficiency.

    Serial Dilution:

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR. .. A standard curve for serial dilution of 18S rRNAs was generated similarly.

    Cell Culture:

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: Real Time PCR To examine MARRS and VDR mRNA expression, HL-60 and MV-4-11 cells were cultured in 24-well plates (2 × 105 cells per mL). .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA).

    TaqMan microRNA Assay:

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: .. All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min. .. Relative expression levels for each miR were calculated based upon the expression of RNU66 and differences in gene expression were determined relative to normal breast tissues from reduction mammoplasties using the comparative Ct method described in the ABI Prism 7700 User Bulletin #2 (Applied Biosystems/Life Technologies).

    Digital PCR:

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: .. Assays were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion dPCR and 1 × Taqman Universal PCR mastermix (no Uracil-DNA Glycosylase), Cat no. 4324018 (Life Technologies) for MethyLight dPCR. .. All reactions also contained 2 × DA sample loading reagent, 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for details of primer and probe design, Additional file for primer and probe sequences, and Additional file for assay performance) and 5 ng DNA.

    Generated:

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: To perform TaqMan qRT-PCR, cDNA was generated from 1 μg patient RNA using the high-capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, 4374966) with RNase inhibitor according to the manufacturer’s recommendation. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR. .. A standard curve for serial dilution of 18S rRNAs was generated similarly.

    Negative Control:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye. .. For each PCR, a mixture containing template cDNA, 1× Master Mix, 200 nM concentrations of each forward and reverse primer, and 250 nM TaqMan probe was applied to a 96-well MicroAmp optical reaction plate with optical caps (Applied Biosystems).

    Sequencing:

    Article Title: PAHSAs enhance hepatic and systemic insulin sensitivity through direct and indirect mechanisms
    Article Snippet: .. Real-time PCRs for G6pc1 and Pck1 were performed on an ABI Prism 7900HT sequence detection system (Applied Biosystems) with TaqMan Universal PCR Master Mix and TaqMan gene expression assays (Applied Biosystems). .. Relative expression levels were determined using the ΔΔCt method.

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells
    Article Snippet: .. TaqMan real-time PCR was carried out in MicroAmp optical 384-well reaction plates (Applied Biosystems) by an ABI Prism 7900HT Sequence Detection System (Applied Biosystems) using TaqMan Universal PCR Master Mix (Applied Biosystems) and following standard “TaqMan” procedures. .. For quantification, target gene expression was normalized by comparison with β- actin expression.

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ). .. It was necessary to sequence a fragment of the cDNA containing part of exon 10 through intron 11 to synthesize a pair of primers adequate to carry out the real-time RT-PCR.

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye. .. Amplification and detection of specific products were performed on the ABI Prism 7700 sequence detection system (PE Biosystems) with the following cycle profile: 1 cycle at 50°C for 2 min, 1 cycle at 95°C for 10 min, 60 cycles at 95°C for 15 s, and 60°C for 1 min.

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ]. .. Amplification and detection were performed using an Applied Biosystems Prism 7900HT sequence detection system with SDS 2.2.1 software (Applied Biosystems) at the following conditions: 2 min at 50°C and 10 min at 95°C, then 45 cycles of 15 s at 95°C and 1 min at 60°C.

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: RT-PCR was performed on the ABI PRISM 7700 sequence detection system using random hexamers from TaqMan reverse transcription reagents and the RT reaction mix (Applied Biosystems, Rockville, M) to reverse-transcribe RNA. .. TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR.

    Software:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: The primers for recA , used as an internal control, were also designed by using Primer Express 1.5 software. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ]. .. Amplification and detection were performed using an Applied Biosystems Prism 7900HT sequence detection system with SDS 2.2.1 software (Applied Biosystems) at the following conditions: 2 min at 50°C and 10 min at 95°C, then 45 cycles of 15 s at 95°C and 1 min at 60°C.

    Fluorescence:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye. .. The critical threshold cycle ( CT ) was defined as the cycle at which the fluorescence becomes detectable above background and is inversely proportional to the logarithm of the initial number of template molecules.

    Mutagenesis:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Total RNA was isolated from S. mutans GS-5 and the luxS mutant by using TRIzol Reagent (Gibco-BRL, Rockville, Md.) according to the manufacturer's instructions. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Isolation:

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: Then, the cells were treated with 1 nM calcitriol or its analogs for 72 h. Total RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol RNA quantity and purity was estimated spectrophotometrically at 260 nm using NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) and the quality of RNA was evaluated by agarose electrophoresis. .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA).

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Total RNA was isolated from S. mutans GS-5 and the luxS mutant by using TRIzol Reagent (Gibco-BRL, Rockville, Md.) according to the manufacturer's instructions. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: The isolated RNA was then used for cDNA synthesis using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). .. Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ].

    Size-exclusion Chromatography:

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: .. All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min. .. Relative expression levels for each miR were calculated based upon the expression of RNU66 and differences in gene expression were determined relative to normal breast tissues from reduction mammoplasties using the comparative Ct method described in the ABI Prism 7700 User Bulletin #2 (Applied Biosystems/Life Technologies).

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: The PCR program was as follows: one cycle of 50°C for 30 min; one cycle of 95°C for 15 min; 45 cycles of 95°C for 15 sec, 55°C for 30 sec, 72°C 30 sec. Each reaction was performed in triplicate for the gene of interest and ACTB for each patient sample. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Labeling:

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: The specific oligonucleotide primer pairs, labeled with a reporter fluorescent dye (FAM) at the 5′ end, and the specific FAM TaqMan probe used for MARRS (PDIA3 assay ID: Hs00607126_m1) and VDR (assay ID: Hs01045840_m1) and a predesigned GAPDH assay used as an endogenous control were obtained from Life Technologies. .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA).

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells
    Article Snippet: TaqMan real-time PCR was carried out in MicroAmp optical 384-well reaction plates (Applied Biosystems) by an ABI Prism 7900HT Sequence Detection System (Applied Biosystems) using TaqMan Universal PCR Master Mix (Applied Biosystems) and following standard “TaqMan” procedures. .. The probe was dual labeled, at the 3′ terminus with a quencher (TAMRA) and at the 5′ terminus with a fluorogenic reporter dye (FAM).

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: The fluorescent probes were labeled with a reporter dye (6-caboxyfluorescein) covalently attached at the 5′ end, and a quencher dye (6-carboxytetramethylrhodamine) covalently attached at the 3′ end. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Purification:

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Single-stranded cDNA was then synthesized in a reaction mixture containing 1.25 U of MultiScribe reverse transcriptase/μl, 0.4 U of RNase inhibitor/μl, 500 mM concentrations of each deoxynucleoside triphosphate, a 200 mM concentration of antisense primer, 1× reverse transcription (RT) buffer, 5.5 mM MgCl2 (TaqMan reverse transcription reagents; Applied Biosystems), and 1.0 μg of total RNA from each phase of culture at 48°C for 30 min. To check for DNA contamination, purified total RNA without reverse transcriptase served as a negative control. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: After reversal of cross-linking, DNA was purified by phenol–chloroform extraction followed by ethanol precipitation. .. Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems).

    Polymerase Chain Reaction:

    Article Title: Induction of the IL-9 gene by HTLV-I Tax stimulates the spontaneous proliferation of primary adult T-cell leukemia cells by a paracrine mechanism
    Article Snippet: .. The Taqman Universal PCR Master Mix, the IL-9 primer/probe, HTLV-I Tax primer/probe, and the HPRT1 primer/probe sets were purchased from Applied Biosystems (Foster City, CA). .. We used Genome Walker Library (Clontech, Mountain View, CA) to clone the IL-9 and IL-9Rα gene 5′ regulatory regions.

    Article Title: PAHSAs enhance hepatic and systemic insulin sensitivity through direct and indirect mechanisms
    Article Snippet: .. Real-time PCRs for G6pc1 and Pck1 were performed on an ABI Prism 7900HT sequence detection system (Applied Biosystems) with TaqMan Universal PCR Master Mix and TaqMan gene expression assays (Applied Biosystems). .. Relative expression levels were determined using the ΔΔCt method.

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: .. Assays were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion dPCR and 1 × Taqman Universal PCR mastermix (no Uracil-DNA Glycosylase), Cat no. 4324018 (Life Technologies) for MethyLight dPCR. .. All reactions also contained 2 × DA sample loading reagent, 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for details of primer and probe design, Additional file for primer and probe sequences, and Additional file for assay performance) and 5 ng DNA.

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA). .. The following protocol were used: 95 °C for 10 min, followed by 40 cycles of two step PCR, including denaturation at 95 °C for 15 s and annealing/extension at 60 °C for 1 min.

    Article Title: The novel histone deacetylase inhibitor, LBH589, induces expression of DNA damage response genes and apoptosis in Ph− acute lymphoblastic leukemia cells
    Article Snippet: .. TaqMan real-time PCR was carried out in MicroAmp optical 384-well reaction plates (Applied Biosystems) by an ABI Prism 7900HT Sequence Detection System (Applied Biosystems) using TaqMan Universal PCR Master Mix (Applied Biosystems) and following standard “TaqMan” procedures. .. For quantification, target gene expression was normalized by comparison with β- actin expression.

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: .. Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ). .. It was necessary to sequence a fragment of the cDNA containing part of exon 10 through intron 11 to synthesize a pair of primers adequate to carry out the real-time RT-PCR.

    Article Title: Dysregulation of microRNA expression drives aberrant DNA hypermethylation in basal-like breast cancer
    Article Snippet: .. All real-time PCR reactions were performed in triplicate using TaqMan Universal PCR Master mix (cat no. 4324018, Applied Biosystems/Life Technologies) in 20 μ l volume containing 10 μ l TaqMan Universal PCR Master mix, 1 μ l of primers and probe mix of the miR-specific TaqMan MicroRNA Assay (Applied Biosystems/Life Technologies), 1.33 μ l of RT product, and 7.67 μ l of nuclease free water and the following amplification conditions: 95°C for 10 min, 40 cycles of 95°C for 15 sec and 60°C for 1 min. .. Relative expression levels for each miR were calculated based upon the expression of RNU66 and differences in gene expression were determined relative to normal breast tissues from reduction mammoplasties using the comparative Ct method described in the ABI Prism 7700 User Bulletin #2 (Applied Biosystems/Life Technologies).

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye. .. For each PCR, a mixture containing template cDNA, 1× Master Mix, 200 nM concentrations of each forward and reverse primer, and 250 nM TaqMan probe was applied to a 96-well MicroAmp optical reaction plate with optical caps (Applied Biosystems).

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: .. Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems). ..

    Article Title: Cellular and molecular basis for stress-induced depression
    Article Snippet: .. Taqman Universal PCR Master Mix (Life Technologies, Foster City, CA, USA) was used for all analyses. .. Taqman gene expression assays (FAM) from Life Technologies were as follows: p11 (Mm00501457_m1) and Gapdh (Mm99999915_g1).

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: .. Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ]. ..

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe. .. The PCR program was as follows: one cycle of 50°C for 2 min; one cycle of 95°C for 10 min; 45 cycles of 95°C for 15 sec, 50°C for 1 min.

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis
    Article Snippet: .. Real-time PCR was performed with TaqMan Universal PCR Master Mix (Applied Biosystems), which contained AmpliTaq Gold DNA polymerase, AmpErase, uracil-N-glycosylase (to prevent contamination from previous qPCR reactions), dNTPs with dUTP, and optimized buffer components. .. Briefly, each sample was run in triplicate design and each 25- μ l reaction mixture consisted of 12.5- μ l of TaqMan Universal PCR Master mix, 400 nM primers, and 300 nM TaqMan probe for each targeted genes as described previously ( ).

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: .. TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR. .. A standard curve for serial dilution of 18S rRNAs was generated similarly.

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: .. Reactions were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion qPCR and 1 × Taqman Universal PCR mastermix without Uracil-DNA Glycosylase, Cat no. 4324018 (Life Technologies) for MethyLight qPCR in a final volume of 20 μL. .. All reactions also contained 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for primer and probe sequences and Additional file for details of assay performance) and 5 ng template DNA.

    Quantitative RT-PCR:

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ). .. It was necessary to sequence a fragment of the cDNA containing part of exon 10 through intron 11 to synthesize a pair of primers adequate to carry out the real-time RT-PCR.

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Paragraph title: Real-time quantitative RT-PCR. ... The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Article Title: Cellular and molecular basis for stress-induced depression
    Article Snippet: Paragraph title: Quantitative RT-PCR ... Taqman Universal PCR Master Mix (Life Technologies, Foster City, CA, USA) was used for all analyses.

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: To perform TaqMan qRT-PCR, cDNA was generated from 1 μg patient RNA using the high-capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, 4374966) with RNase inhibitor according to the manufacturer’s recommendation. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Concentration Assay:

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: Assays were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion dPCR and 1 × Taqman Universal PCR mastermix (no Uracil-DNA Glycosylase), Cat no. 4324018 (Life Technologies) for MethyLight dPCR. .. All reactions also contained 2 × DA sample loading reagent, 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for details of primer and probe design, Additional file for primer and probe sequences, and Additional file for assay performance) and 5 ng DNA.

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ). .. The annealing temperature was 56°C, the extension time 30 s and MgCl2 concentration 2 mM.

    Article Title: LuxS-Based Signaling Affects Streptococcus mutans Biofilm Formation
    Article Snippet: Single-stranded cDNA was then synthesized in a reaction mixture containing 1.25 U of MultiScribe reverse transcriptase/μl, 0.4 U of RNase inhibitor/μl, 500 mM concentrations of each deoxynucleoside triphosphate, a 200 mM concentration of antisense primer, 1× reverse transcription (RT) buffer, 5.5 mM MgCl2 (TaqMan reverse transcription reagents; Applied Biosystems), and 1.0 μg of total RNA from each phase of culture at 48°C for 30 min. To check for DNA contamination, purified total RNA without reverse transcriptase served as a negative control. .. The resulting cDNA and negative control were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems), which contained deoxynucleoside triphosphates with dUTP, Ampli Taq Gold DNA polymerase, Amperase UNG, optimized buffer, and a passive reference dye.

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: Briefly, nuclei were cross-linked with formaldehyde at a final concentration of 1% for 10 min, then digested with 400 units of HindIII (NEB) and ligated under extra-diluted conditions. .. Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems).

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ]. .. For viral load measurement, a standard curve was developed with serial 10-fold dilutions of stock PR8 with a known TCID50 concentration.

    Article Title: Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
    Article Snippet: Reactions were performed using 1 × Taqman Universal PCR mastermix, Cat no. 4304437 (Life Technologies) for RE digestion qPCR and 1 × Taqman Universal PCR mastermix without Uracil-DNA Glycosylase, Cat no. 4324018 (Life Technologies) for MethyLight qPCR in a final volume of 20 μL. .. All reactions also contained 900 nM final concentration forward and reverse primers, 200 nM Probes (see Additional file for primer and probe sequences and Additional file for details of assay performance) and 5 ng template DNA.

    Mouse Assay:

    Article Title: Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
    Article Snippet: Viral loads At various time points post-infection, the lungs of the mice were harvested, weighed, and frozen at −80°C in TRIzol (Invitrogen). .. Real-time assays were performed in triplicate with 5 μl of cDNA, 12.5 μl of 2× TaqMan Universal PCR Master Mix (Applied Biosystems), 900 nM influenza A virus sense primer (5′-AAGACCAATCCTGTCACCTCTGA-3′), 900 nM influenza A virus antisense primer (5′-CAAAGCGTCTACGCTGCAGTCC-3′), and 200 nM influenza A virus probe (FAM-5′-TTTGTGTTCACGCTCACCGT-3′-TAMRA) [ ].

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Structural and functional analysis of the HSP90AA1 gene: distribution of polymorphisms among sheep with different responses to scrapie
    Article Snippet: All RT-PCR reactions were run in duplicate. .. Amplification was carried out in a final volume of 25 μl containing SYBRGreen PCR Master Mix (Applied Biosystems) or TaqMan Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems), depending on the gene analyzed (see ESM Appendix ).

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: The QuantiTect SYBR Green RT-PCR kit (Qiagen, 204143) was used and the 25 μl reaction contained 1× QuantiTect SYBR Green RT-PCR master mix, 1.6 μM each primer, 0.25 μl QuantiTect RT Mix, and 100 ng template RNA. .. PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Article Title: Reconstruction of liver organoid using a bioreactor
    Article Snippet: Paragraph title: Quantitative TaqMan RT-PCR ... TaqMan universal PCR Master Mix and Assays-on-Demand gene expression probes (Applied Biosystems) were used for PCR.

    Electrophoresis:

    Article Title: Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol
    Article Snippet: Then, the cells were treated with 1 nM calcitriol or its analogs for 72 h. Total RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol RNA quantity and purity was estimated spectrophotometrically at 260 nm using NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA) and the quality of RNA was evaluated by agarose electrophoresis. .. Real Time PCR reactions were carried out in a total volume of 10 μL including TaqMan Universal PCR Master Mix, FAM TaqMan probe, forward primer, reverse primer, and TaqMan Universal PCR Master Mix (Applied Biosystems, Foster, CA, USA).

    RNA Extraction:

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis
    Article Snippet: The hippocampus was rapidly dissected for total RNA extraction by using a Trizol reagent (Invitrogen, Carlsbad, CA). cDNA was prepared using the Superscript II first-strand cDNA synthesis kit (Invitrogen). .. Real-time PCR was performed with TaqMan Universal PCR Master Mix (Applied Biosystems), which contained AmpliTaq Gold DNA polymerase, AmpErase, uracil-N-glycosylase (to prevent contamination from previous qPCR reactions), dNTPs with dUTP, and optimized buffer components.

    RNA Expression:

    Article Title: Overexpression of ZNF342 by Juxtaposition with MPO Promoter/Enhancer in the Novel Translocation t(17;19)(q23;q13.32) in Pediatric Acute Myeloid Leukemia and Analysis of ZNF342 Expression in Leukemia
    Article Snippet: Paragraph title: ZNF342 RNA Expression Analysis ... PCR (Applied Biosystems, 4304437) was performed in duplicate with 1 μl of cDNA and either primers for ACTB or ZNF342 in a 25 μl reaction containing 1× TaqMan Universal PCR Master Mix, 500 nM F primer, 500 nM R primer, and 250 nM TaqMan probe.

    Ethanol Precipitation:

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: After reversal of cross-linking, DNA was purified by phenol–chloroform extraction followed by ethanol precipitation. .. Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems).

    Activation Assay:

    Article Title: Estrous Cycle Regulation of Extrasynaptic δ-Containing GABAA Receptor-Mediated Tonic Inhibition and Limbic Epileptogenesis
    Article Snippet: Real-time PCR was performed with TaqMan Universal PCR Master Mix (Applied Biosystems), which contained AmpliTaq Gold DNA polymerase, AmpErase, uracil-N-glycosylase (to prevent contamination from previous qPCR reactions), dNTPs with dUTP, and optimized buffer components. .. The real-time PCR run consisted first of one cycle of 50°C for 2 minutes (AmpErase activation), then one cycle of 95°C for 10 minutes (Taq activation), and 50 cycles of 95°C for 15 seconds and 60°C for 1 minute (denaturation, annealing, and extension).

    BAC Assay:

    Article Title: Molecular determinants for enzalutamide-induced transcription in prostate cancer
    Article Snippet: Real-time PCR was performed using TaqMan® Universal PCR Master Mix (Applied Biosystems). .. BAC RP11-815F2 constructs containing DNA fragments covering the tested regions were used as template controls for normalizing digestion, ligation and primer efficiency.

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    Thermo Fisher taqman universal master mix ii
    Taqman Universal Master Mix Ii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 982 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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