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Illumina Inc truseq rapid sbs kit
Truseq Rapid Sbs Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 62 article reviews
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truseq rapid sbs kit - by Bioz Stars, 2020-02
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Amplification:

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Briefly, the RNA sequencing (RNA-seq) library was prepared through cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: An RNA-seq library was prepared via cDNA amplification, end-repair, 3′ end adenylation, adapter ligation, and amplification. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, an RNA sequencing library was prepared by cDNA amplification, end-repair, 3′ end adenylation, adapter ligation, and amplification. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: After hybridization of the library with bait sequences for 16 h, the captured library was purified and amplified with an index barcode tag and the quality and quantity of the library were measured. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The library was denatured with 0.1 M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell (8 pM), and amplified in situ using TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina). .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Construct:

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: Genomic DNA (250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to construct a library using CancerSCAN , probes and a SureSelect XT reagent kit (HSQ; Agilent Technologies) according to the manufacturer's protocol. .. After the enriched exome libraries were multiplexed, the libraries were sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS kit on the Illumina HiSeq 2500 sequencing platform (Illumina Inc., San Diego, CA).

Article Title: Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Article Snippet: .. Sequencing libraries were constructed for an Illumina HiSeq 2500 systems (Illumina) and sequenced in 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). .. Exome sequencing reads were mapped to the hg19 reference genome using Burrows-Wheeler Aligner (BWA-0.7.5a) .

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Genomic DNA (1 μg) from each sample was sheared using the Covaris S220 (Covaris, Woburn, MA) and used to construct a library using SureSelect XT Human All Exon V5 and a SureSelect XT Reagent Kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: .. Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). ..

Electrophoresis:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The resulting reactions were purified with MinElute columns (Qiagen), after which a final size selection (300–700 bp) was performed by electrophoresis in 2 % agarose. .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Formalin-fixed Paraffin-Embedded:

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Exome sequencing Genomic DNA (1 µg) from each FFPE sample was sheared by Covaris S220 (Covaris, MA, USA) and used for construction of a library with SureSelect XT Human All Exon v5 and the SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer’s protocol. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Expressing:

Article Title: TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection
Article Snippet: Deep sequencing was performed on the Illumina HiSeq 1500 or NextSeq 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer's protocol. .. Gene expression levels were expressed as fragments per kilobase of exon per million mapped sequence reads (FPKM).

Article Title: IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Article Snippet: RNA-seq was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated using Cufflinks software and expressed as fragments per kilobase of exon model per million mapped fragments. .. The RNA-seq data are available at Gene Expression Omnibus database under accession no. GSE100858 .

Hybridization:

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: After hybridization of the library with bait sequences for 16 h, the captured library was purified and amplified with an index barcode tag and the quality and quantity of the library were measured. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Flow Cytometry:

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: .. Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA). .. Captured exomes were sequenced using the Illumina HiSeq 2500 platform, and paired-end 100-bp sequence data were generated.

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The library was denatured with 0.1 M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell (8 pM), and amplified in situ using TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina). .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Ligation:

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Briefly, the RNA sequencing (RNA-seq) library was prepared through cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: An RNA-seq library was prepared via cDNA amplification, end-repair, 3′ end adenylation, adapter ligation, and amplification. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, an RNA sequencing library was prepared by cDNA amplification, end-repair, 3′ end adenylation, adapter ligation, and amplification. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Cell Culture:

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: Naive CD4+ T cells from WT mice were co-infected with retroviruses of pMX-IN/MIT or pMX-IN-HA-Sox5t/MIT-c-Maf for 24 h, and then cultured in neutral conditions for additional 18 h. CD4+ T cells that were co-infected with pMX-IN/MIT or pMX-IN-Sox5t/MIT-c-Maf were isolated and total RNA was prepared from these cells using the PureLink RNA mini kit (Invitrogen). .. Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).

Generated:

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA). .. Captured exomes were sequenced using the Illumina HiSeq 2500 platform, and paired-end 100-bp sequence data were generated.

DNA Sequencing:

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Sequencing:

Article Title: TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection
Article Snippet: .. Deep sequencing was performed on the Illumina HiSeq 1500 or NextSeq 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer's protocol. .. The RNA-seq data were submitted to the NCBI BioSample database ( http://www.ncbi.nlm.nih.gov/biosample ), and the accession numbers are GSM2253673 - GSM2253676.

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina). .. RNA-seq data analysis Reads from FASTQ format files were mapped against the mouse reference genome (UCSC mm10) using TopHat version 2.0.6 with default parameters ( http://ccb.jhu.edu/software/tophat/index.shtml ).

Article Title: Clinical Relevance of Genomic Changes in Recurrent Pediatric Solid Tumors
Article Snippet: .. After the enriched exome libraries were multiplexed, the libraries were sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS kit on the Illumina HiSeq 2500 sequencing platform (Illumina Inc., San Diego, CA). .. The DNA sequence data were aligned to the human genome reference (hg19) using the MEM algorithm in BWA 0.7.5 .

Article Title: Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Article Snippet: .. Sequencing libraries were constructed for an Illumina HiSeq 2500 systems (Illumina) and sequenced in 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). .. Exome sequencing reads were mapped to the hg19 reference genome using Burrows-Wheeler Aligner (BWA-0.7.5a) .

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Paragraph title: Whole-exome sequencing ... Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina). .. RNA-Seq data analysis The reads from the FASTQ files were mapped against the hg19 human reference genome using TopHat version 2.0.6 ( http://ccb.jhu.edu/software/tophat/index.shtml ).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina). .. RNA-seq Data Analysis Reads from the FASTQ files were mapped to the hg19 human reference genome using STAR version 2.5.0a in 2-pass mode , and gene quantification was performed using RSEM .

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Whole transcriptome sequencing Library construction for whole transcriptome sequencing was performed using a Truseq RNA sample preparation v2 kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina). ..

Article Title: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Article Snippet: Paragraph title: Whole-genome sequencing ... A TruSeq Rapid PE Cluster Kit (Illumina), and one-and-a-half TruSeq Rapid SBS Kit (200 cycles, Illumina), were used to perform a 162-bp, paired-end read in Rapid-Run Mode.

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: .. Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments). .. Integration of ChIP-seq data and RNA-seq data.

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: .. Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). ..

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina). ..

Sonication:

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Purified DNA was sheared to an average size of 150 bp in a Covaris Adaptive Focused Acoustics™ (AFA) sonication device (S2, Covaris, Inc., Woburn, MA, USA) and indexed with unique barcode tags using PCR. .. Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

RNA Sequencing Assay:

Article Title: TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection
Article Snippet: Paragraph title: RNA-sequencing (RNA-seq) analysis ... Deep sequencing was performed on the Illumina HiSeq 1500 or NextSeq 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer's protocol.

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Paragraph title: 3. Total RNA extraction and RNA sequencing ... Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Article Snippet: .. RNA-seq was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated using Cufflinks software and expressed as fragments per kilobase of exon model per million mapped fragments. .. An M-A plot was obtained on the basis log ratios and the mean of all transcripts in lung of mice treated with IL-22 and PBS or lung of HDM-sensitized and HDM-challenged WT mice and IL22 −/− mice.

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: Paragraph title: RNA sequencing ... Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Paragraph title: RNA Sequencing ... Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: Paragraph title: RNA-seq analysis. ... Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).

Isolation:

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Isolated total RNA (2 μg) was used for reverse transcription reactions with poly (dT) primers and SuperScriptTM II reverse transcriptase (Invitrogen/Life Technologies, Grand Island, NY, USA) according to the manufacturer’s protocols. .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Article Snippet: RNA-seq analysis Total RNA was isolated from the lung of C57BL/6 mice administered intratracheally with IL-22 (100 ng) or PBS and the lung of WT mice or IL22 −/− mice sensitized and challenged with HDM by using the RNeasy Mini kit (QIAGEN). .. RNA-seq was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated using Cufflinks software and expressed as fragments per kilobase of exon model per million mapped fragments.

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: Isolated total RNA was used in a reverse transcription reaction with poly (dT) primers, using SuperScriptTM II Reverse Transcriptase (Invitrogen/Life Technologies, USA), according to the manufacturer’s protocol. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Isolated total RNA was used in a reverse transcription reaction with poly (dT) primers, using SuperScript II Reverse Transcriptase (Invitrogen/Life Technologies) according to the manufacturer’s protocol. .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: Naive CD4+ T cells from WT mice were co-infected with retroviruses of pMX-IN/MIT or pMX-IN-HA-Sox5t/MIT-c-Maf for 24 h, and then cultured in neutral conditions for additional 18 h. CD4+ T cells that were co-infected with pMX-IN/MIT or pMX-IN-Sox5t/MIT-c-Maf were isolated and total RNA was prepared from these cells using the PureLink RNA mini kit (Invitrogen). .. Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).

Mouse Assay:

Article Title: IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Article Snippet: RNA-seq analysis Total RNA was isolated from the lung of C57BL/6 mice administered intratracheally with IL-22 (100 ng) or PBS and the lung of WT mice or IL22 −/− mice sensitized and challenged with HDM by using the RNeasy Mini kit (QIAGEN). .. RNA-seq was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated using Cufflinks software and expressed as fragments per kilobase of exon model per million mapped fragments.

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: Naive CD4+ T cells from WT mice were co-infected with retroviruses of pMX-IN/MIT or pMX-IN-HA-Sox5t/MIT-c-Maf for 24 h, and then cultured in neutral conditions for additional 18 h. CD4+ T cells that were co-infected with pMX-IN/MIT or pMX-IN-Sox5t/MIT-c-Maf were isolated and total RNA was prepared from these cells using the PureLink RNA mini kit (Invitrogen). .. Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).

Polymerase Chain Reaction:

Article Title: Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Article Snippet: Sequencing libraries were constructed for an Illumina HiSeq 2500 systems (Illumina) and sequenced in 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). .. PCR duplicates were removed by picard-1.93 ( http://broadinstitute.github.io/picard ).

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Purified DNA was sheared to an average size of 150 bp in a Covaris Adaptive Focused Acoustics™ (AFA) sonication device (S2, Covaris, Inc., Woburn, MA, USA) and indexed with unique barcode tags using PCR. .. Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: Immunoprecipitated fragments (5 μL) were subjected to 14 cycles of PCR using single-end PCR primers (Illumina). .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Concentration Assay:

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: The quality and concentration of the library were measured using Bioanalyzer and Qubit instruments, respectively. .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Article Snippet: We utilized the index ratio determined by the MiSeq sequencer, as a relative concentration to determine the run condition for the HiSeq run. .. A TruSeq Rapid PE Cluster Kit (Illumina), and one-and-a-half TruSeq Rapid SBS Kit (200 cycles, Illumina), were used to perform a 162-bp, paired-end read in Rapid-Run Mode.

Purification:

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Purified DNA was sheared to an average size of 150 bp in a Covaris Adaptive Focused Acoustics™ (AFA) sonication device (S2, Covaris, Inc., Woburn, MA, USA) and indexed with unique barcode tags using PCR. .. Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

Article Title: Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers
Article Snippet: After hybridization of the library with bait sequences for 16 h, the captured library was purified and amplified with an index barcode tag and the quality and quantity of the library were measured. .. Sequencing of the exome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: After hybridization of the library with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag, and library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The resulting reactions were purified with MinElute columns (Qiagen), after which a final size selection (300–700 bp) was performed by electrophoresis in 2 % agarose. .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Software:

Article Title: IL-22 induces Reg3γ and inhibits allergic inflammation in house dust mite–induced asthma models
Article Snippet: .. RNA-seq was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated using Cufflinks software and expressed as fragments per kilobase of exon model per million mapped fragments. .. An M-A plot was obtained on the basis log ratios and the mean of all transcripts in lung of mice treated with IL-22 and PBS or lung of HDM-sensitized and HDM-challenged WT mice and IL22 −/− mice.

Article Title: Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Article Snippet: In addition to qMiSeq, an electrophoretic analysis using the Fragment Analyzer (Advanced Analytical) software was performed as a part of the library QC. .. A TruSeq Rapid PE Cluster Kit (Illumina), and one-and-a-half TruSeq Rapid SBS Kit (200 cycles, Illumina), were used to perform a 162-bp, paired-end read in Rapid-Run Mode.

Article Title: Sox5 and c-Maf cooperatively induce Th17 cell differentiation via RORγt induction as downstream targets of Stat3
Article Snippet: .. Sequencing was performed on an Illumina HiSeq1500 using a TruSeq Rapid SBS kit (Illumina) in a 50-base single-end mode. mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments). .. Integration of ChIP-seq data and RNA-seq data.

Real-time Polymerase Chain Reaction:

Article Title: Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Article Snippet: Prepared libraries were assessed for quality and quantity using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), 2100 Bioanalyzer (Agilent Inc., Palo Alto, CA, USA), and Mx3005P qPCR (Agilent Technologies, Inc). .. Samples were multiplexed and flow-cell clusters were created using the TruSeq Rapid Cluster kit and TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: An aliquot of each library was diluted in elution buffer (Qiagen) to 5 ng/μL, and 1 μL was used in real-time PCR reactions to confirm the enrichment for hydroxymethylated region. .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

RNA Extraction:

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Paragraph title: 3. Total RNA extraction and RNA sequencing ... Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Selection:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The resulting reactions were purified with MinElute columns (Qiagen), after which a final size selection (300–700 bp) was performed by electrophoresis in 2 % agarose. .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Sample Prep:

Article Title: TET2 functions as a resistance factor against DNA methylation acquisition during Epstein-Barr virus infection
Article Snippet: RNA-sequencing (RNA-seq) analysis Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), following the manufacturer's protocol. .. Deep sequencing was performed on the Illumina HiSeq 1500 or NextSeq 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer's protocol.

Article Title: IL-10 Plays a Pivotal Role in Tamoxifen-Induced Spasmolytic Polypeptide-Expressing Metaplasia in Gastric Mucosa
Article Snippet: Library construction for whole transcriptome sequencing was performed using the TruSeq RNA sample preparation v2 kit (Illumina, San Diego, CA, USA). .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit (Illumina).

Article Title: Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Article Snippet: RNA sequencing Library construction for RNA sequencing (RNA-seq) was performed using a Truseq RNA Sample Preparation v2 Kit (Illumina). .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: RNA Sequencing Library construction for RNA sequencing was performed using a Truseq RNA Sample Preparation v2 Kit (Illumina). .. Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

In Situ:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: The library was denatured with 0.1 M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell (8 pM), and amplified in situ using TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina). .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Next-Generation Sequencing:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: Paragraph title: DNA hydroxymethylation enrichment by immunoprecipitation and next-generation sequencing: hMeDIP-seq ... High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

Immunoprecipitation:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: Paragraph title: DNA hydroxymethylation enrichment by immunoprecipitation and next-generation sequencing: hMeDIP-seq ... High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina).

High Throughput Screening Assay:

Article Title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis
Article Snippet: .. High-throughput sequencing was performed on the HiSeq 2000 (Illumina) using the TruSeq Rapid SBS Kit (#FC-402-4001, Illumina). ..

Variant Assay:

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). .. Sites potentially harbouring small insertions or deletions were realigned and recalibrated by applying the modules of GATK-3.2 (ref. ) with known variant sites identified from phase I of the 1000 Genomes Project ( http://www.1000genomes.org/ ) and dbSNP-137 ( http://www.ncbi.nlm.nih.gov/SNP/ ).

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    Illumina Inc truseq rapid sbs kit
    Truseq Rapid Sbs Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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