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Illumina Inc truseq rapid pe cluster kit
Truseq Rapid Pe Cluster Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 97/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/truseq rapid pe cluster kit/product/Illumina Inc
Average 97 stars, based on 39 article reviews
Price from $9.99 to $1999.99
truseq rapid pe cluster kit - by Bioz Stars, 2019-10
97/100 stars

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Amplification:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: End repair, dA tailing, and sequencing adapter ligation were performed, followed by cDNA purification with AMPure XP beads (Beckman Coulter) and 12 cycles of polymerase chain reaction (PCR) amplification. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster 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: 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: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: After the library was hybridized with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag. .. 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, San Diego, CA, USA).

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: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: After hybridization of the library with bait sequences for 16 hr, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: Briefly, a RNA sequencing library was prepared through cDNA amplification, end-repair, adenylate 3′ends, adapter ligation, and amplification. .. Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA).

Construct:

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: Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon
Article Snippet: Libraries for stranded-RNA sequencing were constructed using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina K.K., Tokyo, Japan) according to the manufacturer’s instructions (TruSeq Stranded mRNA Sample Preparation Guide Rev. .. Clonal clusters of the libraries were generated using cBot with a TruSeq Rapid PE Cluster Kit (Illumina K.K.) and sequenced using a Hiseq2500 sequencer with a TruSeq Rapid SBS Kit paired-end sequencing method to obtain 100-bp sequences.

Article Title: Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Article Snippet: Both tumor and blood DNA were enriched for exonic regions using the SureSelect XT regent kit (G9611B, Agilent) and SureSelect XT Human All Exon V5 kit (5190-6210, Agilent). .. 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: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: Exomes were captured using the SureSelect XT Human All Exon V5 kit (5190-6208, Agilent). .. 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). .. Exome-sequencing reads were aligned to the hg19 reference genome using BWA-0.7.10 (ref. ).

Formalin-fixed Paraffin-Embedded:

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Paragraph title: Genomic DNA preparation from FFPE tissues for WES ... Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Hybridization:

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: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: After hybridization of the library with bait sequences for 16 hr, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Flow Cytometry:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Libraries were then denatured using sodium hydroxide (NaOH) and diluted to a final concentration of 20 pM. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina). .. After cluster generation, cDNA libraries were sequenced by 2 × 125 paired-end sequencing on an Illumina HiSeq.

Ligation:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: End repair, dA tailing, and sequencing adapter ligation were performed, followed by cDNA purification with AMPure XP beads (Beckman Coulter) and 12 cycles of polymerase chain reaction (PCR) amplification. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster 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).

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: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through the following processes: genomic DNA 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, San Diego, CA, USA).

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: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by genomic DNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
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 performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: Briefly, a RNA sequencing library was prepared through cDNA amplification, end-repair, adenylate 3′ends, adapter ligation, and amplification. .. Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA).

Generated:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Libraries were then denatured using sodium hydroxide (NaOH) and diluted to a final concentration of 20 pM. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina). .. After cluster generation, cDNA libraries were sequenced by 2 × 125 paired-end sequencing on an Illumina HiSeq.

Article Title: Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon
Article Snippet: The libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies Japan). .. Clonal clusters of the libraries were generated using cBot with a TruSeq Rapid PE Cluster Kit (Illumina K.K.) and sequenced using a Hiseq2500 sequencer with a TruSeq Rapid SBS Kit paired-end sequencing method to obtain 100-bp sequences. .. The FASTQ file of the sequence data was generated using HCS v2.0.12, Real time analysis v1.17.21.3, and Consensus Assessment of Sequence and Variation v1.8.2 (Illumina K.K.).

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

DNA HS Assay:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Subsequently, PCR products with lengths of 350–450 bp were selected in 2% agarose gel and quantified with QUBIT DNA HS Assay Kit (Invitrogen Corporation, Carlsbad, CA). .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

DNA Sequencing:

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).

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through the following processes: genomic DNA 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, San Diego, CA, USA).

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared by genomic DNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
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 performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Sequencing:

Article Title: A somatic reference standard for cancer genome sequencing
Article Snippet: Paragraph title: Library preparation and sequencing ... Libraries were clustered onto HiSeq V3 rapid flowcells using the Illumina TruSeq Rapid PE Cluster Kit (2500; cat#PE-402-4001) and sequenced by synthesis on the HiSeq2500 (rapid mode) for paired 112 bp read lengths using Illumina TruSeq Rapid SBS Kits (2500; cat#FC-402-4002).

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: End repair, dA tailing, and sequencing adapter ligation were performed, followed by cDNA purification with AMPure XP beads (Beckman Coulter) and 12 cycles of polymerase chain reaction (PCR) amplification. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster 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). .. Sequencing data and results are summarized in .

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: Library quality and quantity were measured using the Bioanalyzer and Qubit. .. 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). .. 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: Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon
Article Snippet: The libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies Japan). .. Clonal clusters of the libraries were generated using cBot with a TruSeq Rapid PE Cluster Kit (Illumina K.K.) and sequenced using a Hiseq2500 sequencer with a TruSeq Rapid SBS Kit paired-end sequencing method to obtain 100-bp sequences. .. The FASTQ file of the sequence data was generated using HCS v2.0.12, Real time analysis v1.17.21.3, and Consensus Assessment of Sequence and Variation v1.8.2 (Illumina K.K.).

Article Title: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: After the library was hybridized with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag. .. 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, San Diego, CA, USA). .. The newly identified glutamine:fructose-6-phosphate transaminase 1 (GFPT1 )-ALK fusion gene was detected by targeted cancer panel sequencing, and its respective genomic rearrangement was confirmed by genomic PCR analysis, followed by Sanger sequencing.

Article Title: Isolation, phenotypic characterization and genome wide analysis of a Chlamydomonas reinhardtii strain naturally modified under laboratory conditions: towards enhanced microalgal biomass and lipid production for biofuels
Article Snippet: Paragraph title: Whole genome sequencing and SNPs/indels analysis ... Briefly, DNA libraries and cluster construction were performed using TruSeq DNA PCR free sample Preparation Kit (Illumina, USA), TruSeq Rapid SBS kit (Illumina, USA) and TruSeq Rapid PE Cluster kit (Illumina, USA).

Article Title: Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures
Article Snippet: Both tumor and blood DNA were enriched for exonic regions using the SureSelect XT regent kit (G9611B, Agilent) and SureSelect XT Human All Exon V5 kit (5190-6210, Agilent). .. 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: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: Exomes were captured using the SureSelect XT Human All Exon V5 kit (5190-6208, Agilent). .. 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). .. Exome-sequencing reads were aligned to the hg19 reference genome using BWA-0.7.10 (ref. ).

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). .. 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: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: After hybridization of the library with bait sequences for 16 hr, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Sequencing reads were aligned to the UCSC hg19 reference genome using Burrows-Wheeler Aligner [ ], version 0.6.2 with default settings.

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: The library construction for whole transcriptome sequencing was performed using the TruSeq RNA sample preparation v2 kit (Illumina). .. Sequencing of the transcriptome library was carried out using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. The reads from the FASTQ files were mapped against the GRCh37.75 human reference genome by using STAR ( https://github.com/alexdobin/STAR/releases ) version 2.4.0.

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Sequence reads were mapped to the human genome (hg19) using Burrows-Wheeler Alignment tool.

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: The quality and quantity of the library were measured with a Bioanalyzer and Qubit. .. Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA). .. The reads from the FASTQ files were mapped against the hg19 human reference genome using TopHat version 2.0.6 ( http://tophat.cbcb.umd.edu/ ).

Sonication:

Article Title: A somatic reference standard for cancer genome sequencing
Article Snippet: Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation. .. Libraries were clustered onto HiSeq V3 rapid flowcells using the Illumina TruSeq Rapid PE Cluster Kit (2500; cat#PE-402-4001) and sequenced by synthesis on the HiSeq2500 (rapid mode) for paired 112 bp read lengths using Illumina TruSeq Rapid SBS Kits (2500; cat#FC-402-4002).

Multiplexing:

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: For bulk WES, genomic DNA (1 µo) from the BM and matching blood samples was sheared by Covaris S220 (Covaris) and used for library construction with SureSelect XT human all exon v5 and SureSelect XT reagent kit, HSQ (Agilent Technologies) according to the manufacturer's protocols. .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

RNA Sequencing Assay:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Libraries were then denatured using sodium hydroxide (NaOH) and diluted to a final concentration of 20 pM. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina). .. After cluster generation, cDNA libraries were sequenced by 2 × 125 paired-end sequencing on an Illumina HiSeq.

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: Overexpression of p54nrb/NONO induces differential EPHA6 splicing and contributes to castration-resistant prostate cancer growth
Article Snippet: RNA quality was assessed by Nanodrop measurement (Thermo Fisher Scientific). .. RNA-sequencing (RNA-Seq) libraries were prepared using TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS kit (Illumina). .. The libraries were sequenced on Illumina HiSeq 2500 using a read length of 2 × 150 bp.

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: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: Paragraph title: RNA sequencing and data analysis ... Sequencing of the transcriptome 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: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: Paragraph title: RNA Sequencing ... Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA).

Isolation:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Paragraph title: RNA isolation, cDNA library preparation, and RNA-seq ... Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster 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: 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: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: Matching blood DNA was isolated by the QIAamp DNA blood kit (Qiagen). .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: Isolated total RNA (2 µg) was used in a reverse transcription reaction with poly (dT) primers using the SuperScriptTM II reverse transcriptase (Invitrogen/Life Technologies, Grand Island, NY, USA) according to the manufacturer’s protocols. .. Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA).

Purification:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Then, the libraries were purified by AMPure XP beads (Beckman Coulter). .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster 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: Identification of Driving ALK Fusion Genes and Genomic Landscape of Medullary Thyroid Cancer
Article Snippet: After the library was hybridized with bait sequences for 16 hours, the captured library was purified and amplified with an index barcode tag. .. 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, San Diego, CA, USA).

Article Title: Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma
Article Snippet: After hybridization of the library with bait sequences for 16 hr, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was carried out using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Article Title: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: From the CD138− enriched cells, genomic DNA and RNA was purified using the AllPrep kit (Qiagen). .. After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina).

Article Title: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. .. Sequencing of the exome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

Polymerase Chain Reaction:

Article Title: A somatic reference standard for cancer genome sequencing
Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; cat#FC-121-3001) following the manufacturer’s protocol. .. Libraries were clustered onto HiSeq V3 rapid flowcells using the Illumina TruSeq Rapid PE Cluster Kit (2500; cat#PE-402-4001) and sequenced by synthesis on the HiSeq2500 (rapid mode) for paired 112 bp read lengths using Illumina TruSeq Rapid SBS Kits (2500; cat#FC-402-4002).

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Subsequently, PCR products with lengths of 350–450 bp were selected in 2% agarose gel and quantified with QUBIT DNA HS Assay Kit (Invitrogen Corporation, Carlsbad, CA). .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

Article Title: Isolation, phenotypic characterization and genome wide analysis of a Chlamydomonas reinhardtii strain naturally modified under laboratory conditions: towards enhanced microalgal biomass and lipid production for biofuels
Article Snippet: A schematic workflow for the genome sequencing and SNPs/indels analysis was presented in Additional file 3: Figure S2. .. Briefly, DNA libraries and cluster construction were performed using TruSeq DNA PCR free sample Preparation Kit (Illumina, USA), TruSeq Rapid SBS kit (Illumina, USA) and TruSeq Rapid PE Cluster kit (Illumina, USA). .. The C. reinhardtii DNA libraries were sequenced using Illumina HiSeq 2500 (Illumina, USA).

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) .

cDNA Library Assay:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Paragraph title: RNA isolation, cDNA library preparation, and RNA-seq ... Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

Agarose Gel Electrophoresis:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Subsequently, PCR products with lengths of 350–450 bp were selected in 2% agarose gel and quantified with QUBIT DNA HS Assay Kit (Invitrogen Corporation, Carlsbad, CA). .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

Chloramphenicol Acetyltransferase Assay:

Article Title: A somatic reference standard for cancer genome sequencing
Article Snippet: Final libraries were evaluated on the Agilent Bioanalyzer and quantitated by Qubit. .. Libraries were clustered onto HiSeq V3 rapid flowcells using the Illumina TruSeq Rapid PE Cluster Kit (2500; catPE-402-4001) and sequenced by synthesis on the HiSeq2500 (rapid mode) for paired 112 bp read lengths using Illumina TruSeq Rapid SBS Kits (2500; cat#FC-402-4002). .. Pipeline analysis is triggered when data is written from the sequencer to the analysis server in the form of BCL files.

Chromatin Immunoprecipitation:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Quality of cDNA library was evaluated by 2100 Bioanalyzer chip (Agilent). .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

Software:

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/ ).

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).

Sample Prep:

Article Title: A somatic reference standard for cancer genome sequencing
Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; cat#FC-121-3001) following the manufacturer’s protocol. .. Libraries were clustered onto HiSeq V3 rapid flowcells using the Illumina TruSeq Rapid PE Cluster Kit (2500; cat#PE-402-4001) and sequenced by synthesis on the HiSeq2500 (rapid mode) for paired 112 bp read lengths using Illumina TruSeq Rapid SBS Kits (2500; cat#FC-402-4002).

Article Title: Molecular Characterization of Colorectal Signet-Ring Cell Carcinoma Using Whole-Exome and RNA Sequencing
Article Snippet: 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).

Article Title: Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon
Article Snippet: Libraries for stranded-RNA sequencing were constructed using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina K.K., Tokyo, Japan) according to the manufacturer’s instructions (TruSeq Stranded mRNA Sample Preparation Guide Rev. .. Clonal clusters of the libraries were generated using cBot with a TruSeq Rapid PE Cluster Kit (Illumina K.K.) and sequenced using a Hiseq2500 sequencer with a TruSeq Rapid SBS Kit paired-end sequencing method to obtain 100-bp sequences.

Article Title: Isolation, phenotypic characterization and genome wide analysis of a Chlamydomonas reinhardtii strain naturally modified under laboratory conditions: towards enhanced microalgal biomass and lipid production for biofuels
Article Snippet: A schematic workflow for the genome sequencing and SNPs/indels analysis was presented in Additional file 3: Figure S2. .. Briefly, DNA libraries and cluster construction were performed using TruSeq DNA PCR free sample Preparation Kit (Illumina, USA), TruSeq Rapid SBS kit (Illumina, USA) and TruSeq Rapid PE Cluster kit (Illumina, USA). .. The C. reinhardtii DNA libraries were sequenced using Illumina HiSeq 2500 (Illumina, USA).

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: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
Article Snippet: After multiplexing, the libraries were sequenced on the HiSeq 2500 sequencing platform (Illumina), using the 100-bp paired-end mode of the TruSeq Rapid PE cluster kit and TruSeq rapid SBS kit (Illumina). .. For scRNA-seq, CD138-enriched cells were subjected to single cell capture and cDNA amplification using the C1 single-cell auto prep system (Fluidigm) with the SMARTer kit (Clontech).

Article Title: Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
Article Snippet: The library construction for whole transcriptome sequencing was performed using the TruSeq RNA sample preparation v2 kit (Illumina). .. Sequencing of the transcriptome 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: Genomic alterations of ground-glass nodular lung adenocarcinoma
Article Snippet: The library construction for whole transcriptome analyses were performed using the TruSeq RNA sample preparation v2 kit (Illumina, USA). .. Sequencing of the transcriptome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina, USA).

Concentration Assay:

Article Title: Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination
Article Snippet: Libraries were then denatured using sodium hydroxide (NaOH) and diluted to a final concentration of 20 pM. .. Finally, clusters for RNA-seq were generated on flow cell using TruSeq Rapid PE Cluster Kit (Illumina).

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).

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). .. 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).

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    Illumina Inc truseq rapid pe cluster kit
    Truseq Rapid Pe Cluster Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 97/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq rapid pe cluster kit hs
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