Structured Review

Thermo Fisher cdna
Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1044 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 1044 article reviews
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cdna - by Bioz Stars, 2020-01
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Related Articles

Amplification:

Article Title: Inhibition of the RhoGTPase Cdc42 by ML141 enhances hepatocyte differentiation from human adipose-derived mesenchymal stem cells via the Wnt5a/PI3K/miR-122 pathway: impact of the age of the donor
Article Snippet: .. The mRNA was reverse transcribed to complementary DNA (cDNA). cDNA was amplified using VeriQuest Fast SYBR Green qPCR Master Mix (75,690 500 RXN, Affymetrix). .. Thermal cycling was performed on a LightCycler 2.0 (Roche) with the following protocol: 1 cycle (50 °C/2 min), 1 cycle (95 °C/5 min), 45 cycles (95°C/3 s and 60°C/30s).

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard. .. RNA and DNA values were calculated at maximum amplification efficiency, with a slope within the range of −3.30 to −3.32 plotted for each standard curve.

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA). .. Expression levels of beta actin in each samples were examined by 25 cycles of PCR reaction; expression levels of two PAX5 downstream target genes, Blk and BCAR3 genes, were also examined by 30 and 32 cycles of PCR amplification, respectively.

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: .. Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers. .. Primer sequences were determined using Primer3 software from the Internet .

Stable Transfection:

Article Title: Low Levels of Sox2 are required for Melanoma Tumor-Repopulating Cell Dormancy
Article Snippet: .. Transfection and stable cell line generation Cells were transfected with gRNA-Cas9, shRNA, or complementary DNA using Lipofectamine 2000 (Invitrogen) following the manufacturer's protocol. .. Sox2 shRNAs and scramble shRNA sequences are shown in Table .

Synthesized:

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: .. Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Oligonucleotide PCR primers for MyHC- β , α , IIA, IIX, IIB, perinatal, and MyHC-EO gene message ( ) were selected from GenBank mRNA sequences using Oligo 6 software and synthesized by a commercial source (Invitrogen). .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: .. qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Quantitative RT-PCR:

Article Title: Inhibition of the RhoGTPase Cdc42 by ML141 enhances hepatocyte differentiation from human adipose-derived mesenchymal stem cells via the Wnt5a/PI3K/miR-122 pathway: impact of the age of the donor
Article Snippet: Paragraph title: Quantitative real-time polymerase chain reaction (RT-qPCR) ... The mRNA was reverse transcribed to complementary DNA (cDNA). cDNA was amplified using VeriQuest Fast SYBR Green qPCR Master Mix (75,690 500 RXN, Affymetrix).

Article Title: Viral RNA and DNA Trigger Common Antiviral Responses in Mesangial Cells
Article Snippet: Paragraph title: Real-Time RT-PCR ... Complementary DNA was generated from total RNA using random priming and Moloney murine leukemia virus reverse transcriptase (Invitrogen).

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: .. The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA). .. The predesigned TaqMan primer and probe sets were obtained from Applied Biosystems to amplify reaction of the Bax, Bcl2, apoptotic marker genes, and ß-actin as a housekeeping gene.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Paragraph title: qRT-PCR analysis ... Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen).

Article Title: FOXM1 targets NBS1 to regulate DNA damage-induced senescence and epirubicin resistance
Article Snippet: .. Complementary DNA generated by Superscript III reverse transcriptase and oligo-dT primers (Invitrogen, USA) was analysed by quantitative real-time PCR (qRT-PCR) as described ( ). ..

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: .. qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Real-time Polymerase Chain Reaction:

Article Title: Inhibition of the RhoGTPase Cdc42 by ML141 enhances hepatocyte differentiation from human adipose-derived mesenchymal stem cells via the Wnt5a/PI3K/miR-122 pathway: impact of the age of the donor
Article Snippet: .. The mRNA was reverse transcribed to complementary DNA (cDNA). cDNA was amplified using VeriQuest Fast SYBR Green qPCR Master Mix (75,690 500 RXN, Affymetrix). .. Thermal cycling was performed on a LightCycler 2.0 (Roche) with the following protocol: 1 cycle (50 °C/2 min), 1 cycle (95 °C/5 min), 45 cycles (95°C/3 s and 60°C/30s).

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: Paragraph title: Analysis of gene expression using real-time PCR ... The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA).

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Article Title: Immune Activations and Viral Tissue Compartmentalization During Progressive HIV-1 Infection of Humanized Mice
Article Snippet: Tissue HIV-1 RNA was first reverse-transcribed to complementary DNA using a cDNA synthesis kit (Invitrogen, MA) ( ). .. HIV-1 DNA and RNA were quantified by semi-nested real-time PCR as previously described ( ).

Article Title: Novel function of FAXDC2 in megakaryopoiesis
Article Snippet: .. RNA preparation and quantitative real-time PCR Total RNA was extracted with Trizol and complementary DNA was prepared with reverse transcriptase by standard procedure following instructions of the manufacturer (Invitrogen, Grand Island, NY, USA). ..

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Paragraph title: Real-time PCR ... Complementary DNA was made from RNA with Superscript III (Life Technologies).

Article Title: FOXM1 targets NBS1 to regulate DNA damage-induced senescence and epirubicin resistance
Article Snippet: .. Complementary DNA generated by Superscript III reverse transcriptase and oligo-dT primers (Invitrogen, USA) was analysed by quantitative real-time PCR (qRT-PCR) as described ( ). ..

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Random Hexamer Labeling:

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: MyHC RNA was quantified by reverse-transcription polymerase chain reaction (RT-PCR) using Titanium One-Step RT-PCR kits (Clontech Laboratories, Mountain View, CA) that were supplemented with 0.4 μ mol/L oligo dT(18 mer), 20 pg/ μ L random hexamer primers, and SYBR Green (Molecular Probes, Inc., Carlsbad, CA). .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Expressing:

Article Title: Inhibition of the RhoGTPase Cdc42 by ML141 enhances hepatocyte differentiation from human adipose-derived mesenchymal stem cells via the Wnt5a/PI3K/miR-122 pathway: impact of the age of the donor
Article Snippet: The mRNA was reverse transcribed to complementary DNA (cDNA). cDNA was amplified using VeriQuest Fast SYBR Green qPCR Master Mix (75,690 500 RXN, Affymetrix). .. Relative changes in expression were calculated after normalization to GAPDH.

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: Paragraph title: Analysis of gene expression using real-time PCR ... The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA).

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Human atrium RNA was obtained from Ambion, Inc. for authentication of α -myosin expression. .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. EGFP-tagged H2AX expression vectors were constructed in a previous study .

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA). .. Expression levels of beta actin in each samples were examined by 25 cycles of PCR reaction; expression levels of two PAX5 downstream target genes, Blk and BCAR3 genes, were also examined by 30 and 32 cycles of PCR amplification, respectively.

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: Relative abundance of selected genes in the fibroblasts from adhesion and normal peritoneum Steady-state levels of mRNA of selected genes that are known to have a role in cellular adhesion, proliferation, migration, apoptosis and demonstrating different expression levels between adhesion and normal fibroblasts in the gene filter experiments were verified further by a previously described semiquantitative RT-PCR method [ ]. .. Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Chloramphenicol Acetyltransferase Assay:

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The sequences of p53, Mdm2, p21, Mdm4, 45S rRNA, and GAPDH are as follows: p53-RT-F: 5′-GAG AGT ATT TCA CCC TCA AGA TCC G-3′, p53-RT-R: 5′-CCC CAC TTT CTT GAC CAT TGT TT-3′; Mdm2-RT-F: 5′-GAT GAG GAT GAT GAG GTC TAT CGG-3′, Mdm2-RT-R: 5′-TCT GGA AGC CAG TTC TCA CGA A-3′; p21-RT-F: 5′-ACT TCC TCT GCC CTG CTG CA-3′, p21-RT-R: 5′-CGC TTG GAG TGA TAG AAA TCT GTC A-3′; Mdm4-RT-F: 5′-TTT ACA GAC AAA TCA GGA TAT AGG TA-3′, Mdm4-RT-R: 5′-GTA CAC TGC CAC TCA TCC TCA-3′; 45S-F: 5′-ACA CGC TGT CCT TTC CCT ATT AAC ACT AAA-3′, 45S-R: 5′-AGT AAA AAG AAT AGG CTG GAC AAG CAA AAC-3′; GAPDH-F: 5′- GCC GCC TGG AGA AAC CTG CC-3′, GAPDH-R: 5′-GGT GGA AGA GTG GGA GTT GC-3′ ( ).

Countercurrent Chromatography:

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The sequences of p53, Mdm2, p21, Mdm4, 45S rRNA, and GAPDH are as follows: p53-RT-F: 5′-GAG AGT ATT TCA CCC TCA AGA TCC G-3′, p53-RT-R: 5′-CCC CAC TTT CTT GAC CAT TGT TT-3′; Mdm2-RT-F: 5′-GAT GAG GAT GAT GAG GTC TAT CGG-3′, Mdm2-RT-R: 5′-TCT GGA AGC CAG TTC TCA CGA A-3′; p21-RT-F: 5′-ACT TCC TCT GCC CTG CTG CA-3′, p21-RT-R: 5′-CGC TTG GAG TGA TAG AAA TCT GTC A-3′; Mdm4-RT-F: 5′-TTT ACA GAC AAA TCA GGA TAT AGG TA-3′, Mdm4-RT-R: 5′-GTA CAC TGC CAC TCA TCC TCA-3′; 45S-F: 5′-ACA CGC TGT CCT TTC CCT ATT AAC ACT AAA-3′, 45S-R: 5′-AGT AAA AAG AAT AGG CTG GAC AAG CAA AAC-3′; GAPDH-F: 5′- GCC GCC TGG AGA AAC CTG CC-3′, GAPDH-R: 5′-GGT GGA AGA GTG GGA GTT GC-3′ ( ).

Transfection:

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Cell sorting and semi-quantitative RT-PCR YFP positive transfected Daudi cells were sorted by FACStar Cell Sorter (Becton, Dickinson and company, Franklin Lakes, NJ). .. Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA).

Article Title: Low Levels of Sox2 are required for Melanoma Tumor-Repopulating Cell Dormancy
Article Snippet: .. Transfection and stable cell line generation Cells were transfected with gRNA-Cas9, shRNA, or complementary DNA using Lipofectamine 2000 (Invitrogen) following the manufacturer's protocol. .. Sox2 shRNAs and scramble shRNA sequences are shown in Table .

Inverse PCR:

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. S121A and S121E mutations of pENTR1A 3 × Flag H2AX were generated by inverse PCR with a Site-Specific Mutagenesis Kit (Toyobo).

Activation Assay:

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA). .. A Step One Plus Real Time PCR Machine was operated according this program: reverse transcriptase for 15 minutes at 48 °C, activation of ampli Taq gold DNA polymerase for 10 minutes at 95 °C, denaturation for 15 seconds at 95 °C and annealing for 1 minute at 60 °C.

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The cycling program was set as follows: 50°C 2 min, 95°C 10 min for the PCR initial activation and 45 cycles of denaturation at 95°C for 15 s, annealing and extension at 60°C for 1 min.

Multiple Displacement Amplification:

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: Analysis of gene expression using real-time PCR MDA-MB-231 cells at a concentration of 1 × 107 was treated with an IC50 concentration of compound C1 (2.5 μg/mL) for periods of 24, 48, and 72 hours. .. The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA).

Generated:

Article Title: Viral RNA and DNA Trigger Common Antiviral Responses in Mesangial Cells
Article Snippet: .. Complementary DNA was generated from total RNA using random priming and Moloney murine leukemia virus reverse transcriptase (Invitrogen). .. Real-time RT-PCR was performed using SYBR Green PCR Master Mix or TaqMan (Applied Biosystems, Weiterstadt, Germany) and analyzed on an AB Prism 7000 analyzer (Applied Biosystems).

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. S121A and S121E mutations of pENTR1A 3 × Flag H2AX were generated by inverse PCR with a Site-Specific Mutagenesis Kit (Toyobo).

Article Title: FOXM1 targets NBS1 to regulate DNA damage-induced senescence and epirubicin resistance
Article Snippet: .. Complementary DNA generated by Superscript III reverse transcriptase and oligo-dT primers (Invitrogen, USA) was analysed by quantitative real-time PCR (qRT-PCR) as described ( ). ..

Polymerase Chain Reaction:

Article Title: Viral RNA and DNA Trigger Common Antiviral Responses in Mesangial Cells
Article Snippet: Complementary DNA was generated from total RNA using random priming and Moloney murine leukemia virus reverse transcriptase (Invitrogen). .. Real-time RT-PCR was performed using SYBR Green PCR Master Mix or TaqMan (Applied Biosystems, Weiterstadt, Germany) and analyzed on an AB Prism 7000 analyzer (Applied Biosystems).

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Thereafter, myosin RNA from samples was quantified in duplicate, 30 ng aliquots of total muscle RNA using a standard protocol for reverse transcription and PCR in all assays ( ). .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: Immune Activations and Viral Tissue Compartmentalization During Progressive HIV-1 Infection of Humanized Mice
Article Snippet: Tissue HIV-1 RNA was first reverse-transcribed to complementary DNA using a cDNA synthesis kit (Invitrogen, MA) ( ). .. The first round of the PCR was performed on a conventional PCR machine (T100 Thermal Cycler, BioRad, CA).

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA). .. Expression levels of beta actin in each samples were examined by 25 cycles of PCR reaction; expression levels of two PAX5 downstream target genes, Blk and BCAR3 genes, were also examined by 30 and 32 cycles of PCR amplification, respectively.

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: .. Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers. .. Primer sequences were determined using Primer3 software from the Internet .

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The cycling program was set as follows: 50°C 2 min, 95°C 10 min for the PCR initial activation and 45 cycles of denaturation at 95°C for 15 s, annealing and extension at 60°C for 1 min.

Article Title: FOXM1 targets NBS1 to regulate DNA damage-induced senescence and epirubicin resistance
Article Snippet: Complementary DNA generated by Superscript III reverse transcriptase and oligo-dT primers (Invitrogen, USA) was analysed by quantitative real-time PCR (qRT-PCR) as described ( ). .. For PCR-primer sequences, see .

Cellular Antioxidant Activity Assay:

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The sequences of p53, Mdm2, p21, Mdm4, 45S rRNA, and GAPDH are as follows: p53-RT-F: 5′-GAG AGT ATT TCA CCC TCA AGA TCC G-3′, p53-RT-R: 5′-CCC CAC TTT CTT GAC CAT TGT TT-3′; Mdm2-RT-F: 5′-GAT GAG GAT GAT GAG GTC TAT CGG-3′, Mdm2-RT-R: 5′-TCT GGA AGC CAG TTC TCA CGA A-3′; p21-RT-F: 5′-ACT TCC TCT GCC CTG CTG CA-3′, p21-RT-R: 5′-CGC TTG GAG TGA TAG AAA TCT GTC A-3′; Mdm4-RT-F: 5′-TTT ACA GAC AAA TCA GGA TAT AGG TA-3′, Mdm4-RT-R: 5′-GTA CAC TGC CAC TCA TCC TCA-3′; 45S-F: 5′-ACA CGC TGT CCT TTC CCT ATT AAC ACT AAA-3′, 45S-R: 5′-AGT AAA AAG AAT AGG CTG GAC AAG CAA AAC-3′; GAPDH-F: 5′- GCC GCC TGG AGA AAC CTG CC-3′, GAPDH-R: 5′-GGT GGA AGA GTG GGA GTT GC-3′ ( ).

Marker:

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA). .. The predesigned TaqMan primer and probe sets were obtained from Applied Biosystems to amplify reaction of the Bax, Bcl2, apoptotic marker genes, and ß-actin as a housekeeping gene.

In Vivo:

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Mutagenesis:

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. S121A and S121E mutations of pENTR1A 3 × Flag H2AX were generated by inverse PCR with a Site-Specific Mutagenesis Kit (Toyobo).

Isolation:

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Paragraph title: RNA Isolation and Reverse-Transcription Polymerase Chain Reaction ... Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Real-time PCR Total RNA was isolated from MEF cells with Trizol reagent (Life Technologies). .. Complementary DNA was made from RNA with Superscript III (Life Technologies).

Reverse Transcription Polymerase Chain Reaction:

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Paragraph title: RNA Isolation and Reverse-Transcription Polymerase Chain Reaction ... Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: .. Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA). .. Expression levels of beta actin in each samples were examined by 25 cycles of PCR reaction; expression levels of two PAX5 downstream target genes, Blk and BCAR3 genes, were also examined by 30 and 32 cycles of PCR amplification, respectively.

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: Relative abundance of selected genes in the fibroblasts from adhesion and normal peritoneum Steady-state levels of mRNA of selected genes that are known to have a role in cellular adhesion, proliferation, migration, apoptosis and demonstrating different expression levels between adhesion and normal fibroblasts in the gene filter experiments were verified further by a previously described semiquantitative RT-PCR method [ ]. .. Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Construct:

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: .. Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. To construct H2B-EGFP lentivirus vectors, cDNA of H2B was inserted into a pENTR1A vector containing enhanced grren fluorescent protein (EGFP).

Activated Clotting Time Assay:

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The sequences of p53, Mdm2, p21, Mdm4, 45S rRNA, and GAPDH are as follows: p53-RT-F: 5′-GAG AGT ATT TCA CCC TCA AGA TCC G-3′, p53-RT-R: 5′-CCC CAC TTT CTT GAC CAT TGT TT-3′; Mdm2-RT-F: 5′-GAT GAG GAT GAT GAG GTC TAT CGG-3′, Mdm2-RT-R: 5′-TCT GGA AGC CAG TTC TCA CGA A-3′; p21-RT-F: 5′-ACT TCC TCT GCC CTG CTG CA-3′, p21-RT-R: 5′-CGC TTG GAG TGA TAG AAA TCT GTC A-3′; Mdm4-RT-F: 5′-TTT ACA GAC AAA TCA GGA TAT AGG TA-3′, Mdm4-RT-R: 5′-GTA CAC TGC CAC TCA TCC TCA-3′; 45S-F: 5′-ACA CGC TGT CCT TTC CCT ATT AAC ACT AAA-3′, 45S-R: 5′-AGT AAA AAG AAT AGG CTG GAC AAG CAA AAC-3′; GAPDH-F: 5′- GCC GCC TGG AGA AAC CTG CC-3′, GAPDH-R: 5′-GGT GGA AGA GTG GGA GTT GC-3′ ( ).

Plasmid Preparation:

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard. .. RNA and DNA values were calculated at maximum amplification efficiency, with a slope within the range of −3.30 to −3.32 plotted for each standard curve.

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: .. Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. To construct H2B-EGFP lentivirus vectors, cDNA of H2B was inserted into a pENTR1A vector containing enhanced grren fluorescent protein (EGFP).

Software:

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Oligonucleotide PCR primers for MyHC- β , α , IIA, IIX, IIB, perinatal, and MyHC-EO gene message ( ) were selected from GenBank mRNA sequences using Oligo 6 software and synthesized by a commercial source (Invitrogen). .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA). .. PCR products were photographed and density of each PCR band was measured by NIH image software ( http://rsb.info.nih.gov/nih-image/index.html ).

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers. .. Primer sequences were determined using Primer3 software from the Internet .

SYBR Green Assay:

Article Title: Inhibition of the RhoGTPase Cdc42 by ML141 enhances hepatocyte differentiation from human adipose-derived mesenchymal stem cells via the Wnt5a/PI3K/miR-122 pathway: impact of the age of the donor
Article Snippet: .. The mRNA was reverse transcribed to complementary DNA (cDNA). cDNA was amplified using VeriQuest Fast SYBR Green qPCR Master Mix (75,690 500 RXN, Affymetrix). .. Thermal cycling was performed on a LightCycler 2.0 (Roche) with the following protocol: 1 cycle (50 °C/2 min), 1 cycle (95 °C/5 min), 45 cycles (95°C/3 s and 60°C/30s).

Article Title: Viral RNA and DNA Trigger Common Antiviral Responses in Mesangial Cells
Article Snippet: Complementary DNA was generated from total RNA using random priming and Moloney murine leukemia virus reverse transcriptase (Invitrogen). .. Real-time RT-PCR was performed using SYBR Green PCR Master Mix or TaqMan (Applied Biosystems, Weiterstadt, Germany) and analyzed on an AB Prism 7000 analyzer (Applied Biosystems).

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: MyHC RNA was quantified by reverse-transcription polymerase chain reaction (RT-PCR) using Titanium One-Step RT-PCR kits (Clontech Laboratories, Mountain View, CA) that were supplemented with 0.4 μ mol/L oligo dT(18 mer), 20 pg/ μ L random hexamer primers, and SYBR Green (Molecular Probes, Inc., Carlsbad, CA). .. Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. RT-PCR was performed using SYBR Green (biorad), the Applied Biosystems StepOnePlus Real-Time PCR systems, and the primer pairs described in the extended experimental procedures (see ).

RNA Extraction:

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: The RNA extraction for both treated and untreated cells was performed using an RNeasy Plus Mini Kit (Qiagen, Germany). .. The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA).

Article Title: Immune Activations and Viral Tissue Compartmentalization During Progressive HIV-1 Infection of Humanized Mice
Article Snippet: Nucleic Acid Extraction and Quantification Animal tissues were homogenized using a Qiagen Tissue Lyser II followed total nucleic acids (DNA and RNA) extraction with Qiagen All Prep DNA/RNA Mini Kit (QIAGEN). .. Tissue HIV-1 RNA was first reverse-transcribed to complementary DNA using a cDNA synthesis kit (Invitrogen, MA) ( ).

shRNA:

Article Title: Low Levels of Sox2 are required for Melanoma Tumor-Repopulating Cell Dormancy
Article Snippet: .. Transfection and stable cell line generation Cells were transfected with gRNA-Cas9, shRNA, or complementary DNA using Lipofectamine 2000 (Invitrogen) following the manufacturer's protocol. .. Sox2 shRNAs and scramble shRNA sequences are shown in Table .

In Vitro:

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Article Title: A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
Article Snippet: qRT-PCR analysis Total RNA from dissected intact fly thorax, carcass (all of the eggs and intact intestines were removed) and midguts, or S2 cells and MEFs, were extracted using Trizol and complementary DNA synthesized using Superscript II (Invitrogen). .. Results are average ± standard error of at least 3 independent samples, and quantification of gene expression levels calculated using the ΔCt method and normalized to actin5C for all in vivo experiments or rpl32 for all S2 cell in vitro experiments (virus and UV-treatment) or GAPDH for all MEF in vitro experiments.

Electrophoresis:

Article Title: Quantification of Myosin Heavy Chain RNA in Human Laryngeal Muscles: Differential Expression in the Vertical and Horizontal Posterior Cricoarytenoid and Thyroarytenoid
Article Snippet: Input muscle RNA and amplified complementary DNA were quantified from standard curves in each assay using QuantumRNA (Ambion, Inc.) 18S RNA Universal Standards (315 bp) and a plasmid (323 bp) DNA internal standard. .. Amplification products were routinely verified by electrophoresis in 3% NuSieve 3:1 agarose gels containing 0.5 μ g/mL ethidium bromide.

Concentration Assay:

Article Title: Anticancer activity of a monobenzyltin complex C1 against MDA-MB-231 cells through induction of Apoptosis and inhibition of breast cancer stem cells
Article Snippet: Analysis of gene expression using real-time PCR MDA-MB-231 cells at a concentration of 1 × 107 was treated with an IC50 concentration of compound C1 (2.5 μg/mL) for periods of 24, 48, and 72 hours. .. The transcribed cDNA (1 μL) was prepared by converting the total RNA to cDNA using a Two-Step qRT-PCR Kit, High capacity RNA to CDNA- from Applied Biosystems (USA).

Migration:

Article Title: Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum
Article Snippet: Relative abundance of selected genes in the fibroblasts from adhesion and normal peritoneum Steady-state levels of mRNA of selected genes that are known to have a role in cellular adhesion, proliferation, migration, apoptosis and demonstrating different expression levels between adhesion and normal fibroblasts in the gene filter experiments were verified further by a previously described semiquantitative RT-PCR method [ ]. .. Complementary DNA (100 ng) was subjected to PCR amplification of the cDNA of interests in a 25 μl reaction mixture containing 50 mM Tris-HCl (pH 8.4), 50 mM KCl, 2.5 mM MgCl2 , 0.2 mM dNTP, 0.5 U Taq Polymerase (all from Life Technology, BRL) and 1 μM each of sense and antisense primers.

FLAG-tag:

Article Title: Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Article Snippet: .. Plasmid construction To construct Tet-on-inducible lentivirus constructs, complementary DNA of human H2AX and Bub1 was inserted into a pENTR1A vector (Invitrogen) containing 3 × Flag epitope. .. To construct H2B-EGFP lentivirus vectors, cDNA of H2B was inserted into a pENTR1A vector containing enhanced grren fluorescent protein (EGFP).

CTG Assay:

Article Title: Ribosomal protein S27-like is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis
Article Snippet: Complementary DNA was made from RNA with Superscript III (Life Technologies). .. The sequences of p53, Mdm2, p21, Mdm4, 45S rRNA, and GAPDH are as follows: p53-RT-F: 5′-GAG AGT ATT TCA CCC TCA AGA TCC G-3′, p53-RT-R: 5′-CCC CAC TTT CTT GAC CAT TGT TT-3′; Mdm2-RT-F: 5′-GAT GAG GAT GAT GAG GTC TAT CGG-3′, Mdm2-RT-R: 5′-TCT GGA AGC CAG TTC TCA CGA A-3′; p21-RT-F: 5′-ACT TCC TCT GCC CTG CTG CA-3′, p21-RT-R: 5′-CGC TTG GAG TGA TAG AAA TCT GTC A-3′; Mdm4-RT-F: 5′-TTT ACA GAC AAA TCA GGA TAT AGG TA-3′, Mdm4-RT-R: 5′-GTA CAC TGC CAC TCA TCC TCA-3′; 45S-F: 5′-ACA CGC TGT CCT TTC CCT ATT AAC ACT AAA-3′, 45S-R: 5′-AGT AAA AAG AAT AGG CTG GAC AAG CAA AAC-3′; GAPDH-F: 5′- GCC GCC TGG AGA AAC CTG CC-3′, GAPDH-R: 5′-GGT GGA AGA GTG GGA GTT GC-3′ ( ).

FACS:

Article Title: Dominant-Negative Mechanism of Leukemogenic PAX5 Fusions
Article Snippet: Paragraph title: Cell sorting and semi-quantitative RT-PCR ... Total RNA was extracted and complementary DNA was genereated using SuperScript® III One-Step RT-PCR system (Invitrogen, Carlsbad, CA).

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