poly dt oligonucleotide  (Thermo Fisher)


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    Structured Review

    Thermo Fisher poly dt oligonucleotide
    Poly Dt Oligonucleotide, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/poly dt oligonucleotide/product/Thermo Fisher
    Average 95 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    poly dt oligonucleotide - by Bioz Stars, 2020-04
    95/100 stars

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    Related Articles

    Synthesized:

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: .. In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA). .. The first strand cDNA was then used as template for quantitative RT-PCR with the JumpStart Taq ReadyMix kit (Sigma-Aldrich, St. Louis, MO).

    Article Title: Caudal-related Homeobox (Cdx) Protein-dependent Integration of Canonical Wnt Signaling on Paired-box 3 (Pax3) Neural Crest Enhancer *
    Article Snippet: .. Total RNA was isolated from frozen cell pellets by using the RNeasy kit (Qiagen), and cDNA was synthesized using a poly(dT) oligonucleotide and Superscript II reverse transcriptase (Invitrogen) in accordance with manufacturer's protocols. .. PCR amplifications were then performed with Platinum Taq DNA polymerase (Invitrogen) and consisted of 25–35 cycles of 30 s at 96 °C, 30 s at 60 °C, and 45 s at 68 °C.

    Quantitative RT-PCR:

    Article Title: Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia
    Article Snippet: Paragraph title: qRT-PCR and Genomic PCR. ... Total RNA from cells was extracted using RNeasy isolation kit from Qiagen. cDNA was generated using a poly(dT) oligonucleotide and the SuperScript III Reverse Transcriptase (Invitrogen).

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: Paragraph title: Quantitative RT-PCR ... In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA).

    Article Title: BCL6 is critical for the development of a diverse primary B cell repertoire
    Article Snippet: Paragraph title: Quantitative RT-PCR. ... Total RNA from cells was extracted using the RNeasy isolation kit from QIAGEN. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase (Invitrogen).

    SYBR Green Assay:

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. PCR assays were carried out with Corbett 6200/6600 qPCR System using 5 μl cDNA template, 0.25 μM of each primer and Taq polymerase in 1 × SYBR Green Mix.

    Microarray:

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Paragraph title: Generation of cRNA and Microarray Hybridization. ... Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted.

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: Quantitative RT-PCR We performed quantitative RT-PCR in order to: (i) Validate the original microarray observation of differences in FOXO1a gene expression between humans and chimpanzees, (ii) confirm the FOXO1a knockdown in HepG2/C3A liver cells (see below), and (iii) test for inter-species differences expression of the eight FOXO1a direct transcriptional targets (see below). .. In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA).

    Article Title: Anti-fibrotic Activity and Enhanced Interleukin-6 Production by Hepatic Stellate cells in Response to Imatinib Mesylate
    Article Snippet: Paragraph title: Microarray Analysis ... Then, 5 μg RNA were reverse-transcribed using a poly (dT) oligonucleotide (GeneChip®, Invitrogen).

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: Paragraph title: Microarray analysis ... RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen).

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: Paragraph title: Oligonucleotide cDNA microarray analysis ... In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA).

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. The detailed procedures of RNA purification and hybridization for the microarray analyses were as described previously.

    Incubation:

    Article Title: In Vitro Selection of Fab Fragments by mRNA Display and Gene-Linking Emulsion PCR
    Article Snippet: The molecules were then diluted into 175 μ L of Hybridization Buffer (1 M NaCl, 100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 0.25% Triton X-100) and mixed with 100 pmol of poly-dT oligonucleotide with a biotinylated photo-cleavable linker and a high-capacity NeutrAvidin agarose resin (Pierce). .. The resin was then mixed with ReverTra Ace reverse transcriptase (Toyobo) and incubated at 42°C for 30 min. After washing with PBST three times, 40 μ L of elution buffer (PBS with 10% Solution A of PURE system S-S) was added to the resin and exposed to UV radiation at > 300 nm to elute the mRNA-displayed molecules as previously described [ ].

    Expressing:

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted. .. After scanning (scanner from Affymetrix), the expression values for the genes were determined using Affymetrix GENECHIP software, using the Global Scaling option that allows a number of experiments to be normalized to one target intensity, thus facilitating comparison between multiple experiments.

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: Quantitative RT-PCR We performed quantitative RT-PCR in order to: (i) Validate the original microarray observation of differences in FOXO1a gene expression between humans and chimpanzees, (ii) confirm the FOXO1a knockdown in HepG2/C3A liver cells (see below), and (iii) test for inter-species differences expression of the eight FOXO1a direct transcriptional targets (see below). .. In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA).

    Article Title: Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells
    Article Snippet: Total RNA from human leukemia cells was extracted using an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase according to the manufacturer’s protocol (Invitrogen). .. The levels of gene expression were measured using the SYBRGreenER mix (Invitrogen) with primers listed in .

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. Primers used for the measurement of indicated gene expression were as follows: E2-2, 5’-GAGTGTCTCCTCTGGCAGC-3’ and 5’-CCATGTGATTCGATGCGTC-3’; CLEC4C (BDCA2), 5’-ACTGGGATGCAATCTTGGAC-3’ and 5’-GATCTGACAGCCCCAGAAAA-3’; Siglec-6, 5’- AAGGGGCTGATGTTCCAGTG-3’ and 5’- ATGCAGCATTGTCCCTCCTC-3’; TCL1B, 5’-TTCCAGTTTCTGGGAAATAGCAG-3’ and 5’-TCTCCGGCTGATATGTTAGGAC-3’; GZMB, 5’-TACCATTGAGTTGTGCGTGGG-3’ and 5’-GCCATTGTTTCGTCCATAGGAGA-3’.

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. To compare CB versus PB CD56dim gene expression, data from the subsets were imported into GeneSpring GX 10 (Agilent Technologies, Foster City, CA) or Partek Genomics Suite (St. Louis, MO), normalized, and presented as log2 values.

    Hybridization:

    Article Title: In Vitro Selection of Fab Fragments by mRNA Display and Gene-Linking Emulsion PCR
    Article Snippet: .. The molecules were then diluted into 175 μ L of Hybridization Buffer (1 M NaCl, 100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 0.25% Triton X-100) and mixed with 100 pmol of poly-dT oligonucleotide with a biotinylated photo-cleavable linker and a high-capacity NeutrAvidin agarose resin (Pierce). ..

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Paragraph title: Generation of cRNA and Microarray Hybridization. ... Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted.

    Article Title: Anti-fibrotic Activity and Enhanced Interleukin-6 Production by Hepatic Stellate cells in Response to Imatinib Mesylate
    Article Snippet: Then, 5 μg RNA were reverse-transcribed using a poly (dT) oligonucleotide (GeneChip®, Invitrogen). .. Hybridization was conducted using a human genome U133 plus 2.0 array (Affymetrix).

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen). .. These cRNAs were fragmented to sizes ranging from 50 to 200 bases by heating at 94°C for 35 min, and then were used for separate hybridization to a rat Genome U34A Array (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions, with a prior quality assay using Test2 Array probe chips.

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: RNA purification and hybridization for the microarray analyses were performed as previously described ( ). .. In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA).

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. The detailed procedures of RNA purification and hybridization for the microarray analyses were as described previously.

    Infection:

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: RT- PCR and ELISA For E2-2 knockdown, GEN2.2 cells were transduced by lentiviral vectors with or without shRNA for E2-2, and GFP+ cells were sorted at 3–5 days post infection. .. Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr.

    Generated:

    Article Title: Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia
    Article Snippet: .. Total RNA from cells was extracted using RNeasy isolation kit from Qiagen. cDNA was generated using a poly(dT) oligonucleotide and the SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and the ABI7900HT real-time PCR system (Applied Biosystems) according to standard PCR conditions.

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: .. Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted. .. Biotinylated cRNA was generated by in vitro transcription using the Bio Array™ High Yield™ RNA Transcript Labeling kit (ENZO Diagnostics, Inc.).

    Article Title: Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells
    Article Snippet: .. Total RNA from human leukemia cells was extracted using an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase according to the manufacturer’s protocol (Invitrogen). .. The levels of gene expression were measured using the SYBRGreenER mix (Invitrogen) with primers listed in .

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: .. In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Biotinylated labelling of cRNA was performed by in vitro transcription according to manufacturer’s protocol.

    Article Title: BCL6 is critical for the development of a diverse primary B cell repertoire
    Article Snippet: .. Total RNA from cells was extracted using the RNeasy isolation kit from QIAGEN. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and a real-time PCR system (ABI7900HT; Applied Biosystems) according to standard PCR conditions.

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. The detailed procedures of RNA purification and hybridization for the microarray analyses were as described previously.

    Polymerase Chain Reaction:

    Article Title: Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia
    Article Snippet: Paragraph title: qRT-PCR and Genomic PCR. ... Total RNA from cells was extracted using RNeasy isolation kit from Qiagen. cDNA was generated using a poly(dT) oligonucleotide and the SuperScript III Reverse Transcriptase (Invitrogen).

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA). .. For all reactions, PCR primers and probes were designed in sequences that are identical between human and chimpanzee (based on their available genomic sequence ( http://genome.ucsc.edu/ )).

    Article Title: Caudal-related Homeobox (Cdx) Protein-dependent Integration of Canonical Wnt Signaling on Paired-box 3 (Pax3) Neural Crest Enhancer *
    Article Snippet: Total RNA was isolated from frozen cell pellets by using the RNeasy kit (Qiagen), and cDNA was synthesized using a poly(dT) oligonucleotide and Superscript II reverse transcriptase (Invitrogen) in accordance with manufacturer's protocols. .. PCR amplifications were then performed with Platinum Taq DNA polymerase (Invitrogen) and consisted of 25–35 cycles of 30 s at 96 °C, 30 s at 60 °C, and 45 s at 68 °C.

    Article Title: BCL6 is critical for the development of a diverse primary B cell repertoire
    Article Snippet: Total RNA from cells was extracted using the RNeasy isolation kit from QIAGEN. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and a real-time PCR system (ABI7900HT; Applied Biosystems) according to standard PCR conditions.

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. PCR assays were carried out with Corbett 6200/6600 qPCR System using 5 μl cDNA template, 0.25 μM of each primer and Taq polymerase in 1 × SYBR Green Mix.

    Sequencing:

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA). .. For all reactions, PCR primers and probes were designed in sequences that are identical between human and chimpanzee (based on their available genomic sequence ( http://genome.ucsc.edu/ )).

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: .. RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen). .. In vitro RNA transcription was performed to incorporate biotin-labeled ribonucleotides into the cRNA transcripts using an RNA transcript labeling kit (Enzo Biochem, Farmingdale, NY).

    Molecular Cloning:

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: .. Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. PCR assays were carried out with Corbett 6200/6600 qPCR System using 5 μl cDNA template, 0.25 μM of each primer and Taq polymerase in 1 × SYBR Green Mix.

    Isolation:

    Article Title: Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia
    Article Snippet: .. Total RNA from cells was extracted using RNeasy isolation kit from Qiagen. cDNA was generated using a poly(dT) oligonucleotide and the SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and the ABI7900HT real-time PCR system (Applied Biosystems) according to standard PCR conditions.

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Total RNA was isolated in two steps using Trizol (Life Technologies), followed by RNeasy (QIAGEN) purification. .. Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted.

    Article Title: Caudal-related Homeobox (Cdx) Protein-dependent Integration of Canonical Wnt Signaling on Paired-box 3 (Pax3) Neural Crest Enhancer *
    Article Snippet: .. Total RNA was isolated from frozen cell pellets by using the RNeasy kit (Qiagen), and cDNA was synthesized using a poly(dT) oligonucleotide and Superscript II reverse transcriptase (Invitrogen) in accordance with manufacturer's protocols. .. PCR amplifications were then performed with Platinum Taq DNA polymerase (Invitrogen) and consisted of 25–35 cycles of 30 s at 96 °C, 30 s at 60 °C, and 45 s at 68 °C.

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: .. In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Biotinylated labelling of cRNA was performed by in vitro transcription according to manufacturer’s protocol.

    Article Title: BCL6 is critical for the development of a diverse primary B cell repertoire
    Article Snippet: .. Total RNA from cells was extracted using the RNeasy isolation kit from QIAGEN. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and a real-time PCR system (ABI7900HT; Applied Biosystems) according to standard PCR conditions.

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: .. Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. PCR assays were carried out with Corbett 6200/6600 qPCR System using 5 μl cDNA template, 0.25 μM of each primer and Taq polymerase in 1 × SYBR Green Mix.

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: Comparison of CB and PB CD56dim genomics Total RNA from CB CD56dim and PB CD56dim NK cell subsets were isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and then underwent affinity column purification (Qiagen, Valencia, CA). .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix).

    Size-exclusion Chromatography:

    Article Title: A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway
    Article Snippet: In all cases, we synthesized first-strand cDNA using a poly-T oligonucleotide and the Superscript enzyme (Invitrogen, Carlsbad, CA). .. The cycling conditions were as follows: initial denaturation at 94°C for 2 min, following by 40 cycles of denaturation at 94°C for 15 sec and annealing/extension at 60°C for 1 min. β−Actin was used as control for gene expression analyses.

    Labeling:

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted. .. Biotinylated cRNA was generated by in vitro transcription using the Bio Array™ High Yield™ RNA Transcript Labeling kit (ENZO Diagnostics, Inc.).

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen). .. In vitro RNA transcription was performed to incorporate biotin-labeled ribonucleotides into the cRNA transcripts using an RNA transcript labeling kit (Enzo Biochem, Farmingdale, NY).

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. The detailed procedures of RNA purification and hybridization for the microarray analyses were as described previously.

    Purification:

    Article Title: In Vitro Selection of Fab Fragments by mRNA Display and Gene-Linking Emulsion PCR
    Article Snippet: In Vitro Transcription and Translation The DNA templates were transcribed by T7 Ribomax Express Large Scale RNA production system (Promega) and purified by using the RNeasy mini kit (Qiagen). .. The molecules were then diluted into 175 μ L of Hybridization Buffer (1 M NaCl, 100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 0.25% Triton X-100) and mixed with 100 pmol of poly-dT oligonucleotide with a biotinylated photo-cleavable linker and a high-capacity NeutrAvidin agarose resin (Pierce).

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Total RNA was isolated in two steps using Trizol (Life Technologies), followed by RNeasy (QIAGEN) purification. .. Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted.

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: Equal amount of the RNA from each group was taken for purification of poly (A) mRNA by using a poly (A) purification kit (Promega, Madison, WI). .. RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen).

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: .. In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Biotinylated labelling of cRNA was performed by in vitro transcription according to manufacturer’s protocol.

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: Comparison of CB and PB CD56dim genomics Total RNA from CB CD56dim and PB CD56dim NK cell subsets were isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and then underwent affinity column purification (Qiagen, Valencia, CA). .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Caudal-related Homeobox (Cdx) Protein-dependent Integration of Canonical Wnt Signaling on Paired-box 3 (Pax3) Neural Crest Enhancer *
    Article Snippet: Paragraph title: RNA Extraction and RT-PCR Analysis ... Total RNA was isolated from frozen cell pellets by using the RNeasy kit (Qiagen), and cDNA was synthesized using a poly(dT) oligonucleotide and Superscript II reverse transcriptase (Invitrogen) in accordance with manufacturer's protocols.

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Paragraph title: RT- PCR and ELISA ... Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr.

    Affinity Column:

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: .. In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Biotinylated labelling of cRNA was performed by in vitro transcription according to manufacturer’s protocol.

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: Comparison of CB and PB CD56dim genomics Total RNA from CB CD56dim and PB CD56dim NK cell subsets were isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and then underwent affinity column purification (Qiagen, Valencia, CA). .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix).

    Chromatin Immunoprecipitation:

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Fragmented cRNA (15 µg) was hybridized to HG_U133 A2 Gene Chip® arrays (Affymetrix) using Fluidics Station 450 (Affymetrix).

    Article Title: Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells
    Article Snippet: .. Subsequent double-stranded complementary deoxyribonucleic acid (cDNA) was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA), as we have described., Biotinylated labeling cRNA was performed by invitro transcription, , and 15 µg fragmented cRNA was subjected to oligonucleotide hybridization using Fluidics Station 450 (Affymetrix) to human U133A2 gene chip (Affymetrix). .. The detailed procedures of RNA purification and hybridization for the microarray analyses were as described previously.

    Software:

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted. .. After scanning (scanner from Affymetrix), the expression values for the genes were determined using Affymetrix GENECHIP software, using the Global Scaling option that allows a number of experiments to be normalized to one target intensity, thus facilitating comparison between multiple experiments.

    Article Title: Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells
    Article Snippet: Total RNA from human leukemia cells was extracted using an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase according to the manufacturer’s protocol (Invitrogen). .. The reactions were performed using the ABI 7900HT real-time PCR system (Applied Biosystems) and analyzed with the SigmaPlot version 12.0 software program.

    Real-time Polymerase Chain Reaction:

    Article Title: Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia
    Article Snippet: Total RNA from cells was extracted using RNeasy isolation kit from Qiagen. cDNA was generated using a poly(dT) oligonucleotide and the SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and the ABI7900HT real-time PCR system (Applied Biosystems) according to standard PCR conditions.

    Article Title: Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells
    Article Snippet: Total RNA from human leukemia cells was extracted using an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instructions. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase according to the manufacturer’s protocol (Invitrogen). .. The reactions were performed using the ABI 7900HT real-time PCR system (Applied Biosystems) and analyzed with the SigmaPlot version 12.0 software program.

    Article Title: BCL6 is critical for the development of a diverse primary B cell repertoire
    Article Snippet: Total RNA from cells was extracted using the RNeasy isolation kit from QIAGEN. cDNA was generated using a poly(dT) oligonucleotide and SuperScript III Reverse Transcriptase (Invitrogen). .. Quantitative real-time PCR was performed with the SYBRGreenER mix (Invitrogen) and a real-time PCR system (ABI7900HT; Applied Biosystems) according to standard PCR conditions.

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr. .. PCR assays were carried out with Corbett 6200/6600 qPCR System using 5 μl cDNA template, 0.25 μM of each primer and Taq polymerase in 1 × SYBR Green Mix.

    RNA Extraction:

    Article Title: Caudal-related Homeobox (Cdx) Protein-dependent Integration of Canonical Wnt Signaling on Paired-box 3 (Pax3) Neural Crest Enhancer *
    Article Snippet: Paragraph title: RNA Extraction and RT-PCR Analysis ... Total RNA was isolated from frozen cell pellets by using the RNeasy kit (Qiagen), and cDNA was synthesized using a poly(dT) oligonucleotide and Superscript II reverse transcriptase (Invitrogen) in accordance with manufacturer's protocols.

    shRNA:

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: RT- PCR and ELISA For E2-2 knockdown, GEN2.2 cells were transduced by lentiviral vectors with or without shRNA for E2-2, and GFP+ cells were sorted at 3–5 days post infection. .. Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr.

    Agarose Gel Electrophoresis:

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen). .. Labeled cRNAs were purified and analyzed by agarose gel electrophoresis to confirm a size distribution ranging from 500 to 1200 bases.

    In Vitro:

    Article Title: In Vitro Selection of Fab Fragments by mRNA Display and Gene-Linking Emulsion PCR
    Article Snippet: Paragraph title: 3.3. In Vitro Transcription and Translation ... The molecules were then diluted into 175 μ L of Hybridization Buffer (1 M NaCl, 100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 0.25% Triton X-100) and mixed with 100 pmol of poly-dT oligonucleotide with a biotinylated photo-cleavable linker and a high-capacity NeutrAvidin agarose resin (Pierce).

    Article Title: Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells 〉
    Article Snippet: Double strand cDNA was generated from 5 μg of total RNA using a poly dT oligonucleotide that contains a T7 RNA polymerase initiation site and the SuperScript Choice System kit (Life Technologies). cDNA was phenol/chloroform extracted. .. Biotinylated cRNA was generated by in vitro transcription using the Bio Array™ High Yield™ RNA Transcript Labeling kit (ENZO Diagnostics, Inc.).

    Article Title: Molecular mechanism of immune response induced by foreign plasmid DNA after oral administration in mice
    Article Snippet: RNA samples were reverse-transcribed with poly dT oligonucleotide attached to a sequence of the T7 promoter region, digested with RNase H, and copied into dsDNAs (SuperScript Choice System, Invitrogen). .. In vitro RNA transcription was performed to incorporate biotin-labeled ribonucleotides into the cRNA transcripts using an RNA transcript labeling kit (Enzo Biochem, Farmingdale, NY).

    Article Title: Comparative genomic expression signatures of signal transduction pathways and targets in paediatric Burkitt lymphoma (PEBL): A Children’s Oncology Group (COG) report
    Article Snippet: In brief, total RNA from patient tumour specimens was isolated by Trizol reagents (Invitrogen, Carlsbad, CA) and followed by affinity column purification (Qiagen, Valencia, CA). cDNA was generated from 100 ng total RNA using a poly dT oligonucleotide (Affymetrix, Santa Clara, CA). .. Biotinylated labelling of cRNA was performed by in vitro transcription according to manufacturer’s protocol.

    Enzyme-linked Immunosorbent Assay:

    Article Title: Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
    Article Snippet: Paragraph title: RT- PCR and ELISA ... Cells were resuspended in Trizol reagent (Invitrogen), total RNA was isolated according to Molecular Cloning: A Laboratory Manual and reverse transcribed using a poly-dT oligonucleotide (Invitrogen) and M-MLV Reverse Transcriptase (Promega) at 42 °C for 1 hr.

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