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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 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/truseq rapid sbs kit/product/Illumina Inc
Average 99 stars, based on 49 article reviews
Price from $9.99 to $1999.99
truseq rapid sbs kit - by Bioz Stars, 2019-10
99/100 stars

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Amplification:

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: 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: Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Article Snippet: Barcoded cDNAs from multiple samples were then pooled, amplified, and tagmented using a transposon-fragmentation approach that enriches for 3′ ends of cDNA. .. A library of 350–800 base pairs (bp) was run on an Illumina HiSeq 2500 using a 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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: After hybridization of the library with bait sequences for 27 hr, the captured library was purified and amplified with an index barcode tag, and the library's 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 the 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: 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: 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: 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).

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).

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).

Expressing:

Article Title: Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Article Snippet: Paragraph title: Digital gene expression sequencing ... A library of 350–800 base pairs (bp) was run on an Illumina HiSeq 2500 using a TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: After hybridization of the library with bait sequences for 27 hr, the captured library was purified and amplified with an index barcode tag, and the library's 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 the 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: Exomes were targeted using the SureSelect XT Human All Exon V5 kit (Agilent). .. 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.

Ligation:

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: 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: 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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adapter ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
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 the 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: 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 Sequencing:

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: 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: 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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adapter ligation, and amplification. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Article Title: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
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 the TruSeq Rapid SBS kit (Illumina).

Sequencing:

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: 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: 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: 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: 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: Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Article Snippet: Deep sequencing was performed on the Illumina HiSeq. .. 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer’s protocol.

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: Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Article Snippet: Paragraph title: Digital gene expression sequencing ... A library of 350–800 base pairs (bp) was run on an Illumina HiSeq 2500 using a 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: 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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina). .. We performed intrinsic subtyping with log-scaled normalized expression values using the 50-gene Prediction Analysis of Microarray (PAM50) subtype predictor as described by Parker et al. [ ].

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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: After hybridization of the library with bait sequences for 27 hr, the captured library was purified and amplified with an index barcode tag, and the library's 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 the TruSeq Rapid SBS kit (Illumina). .. Sequence reads were mapped to the human genome (hg19) using the Burrows-Wheeler Aligner (BWA) [ ].

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: 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: 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).

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: Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Article Snippet: Paragraph title: Library construction for RNA sequencing (RNA-seq) ... 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer’s protocol.

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: Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Article Snippet: A high-throughput 3′ digital gene expression RNA-sequencing (DGE-seq) protocol was performed as described previously [ ]. .. A library of 350–800 base pairs (bp) was run on an Illumina HiSeq 2500 using a TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

Article Title: Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Article Snippet: Paragraph title: RNA storage, shipment and RNA-seq ... Ribosomal RNA was removed by treatment with the Ribo-Zero rRNA removal kit for bacteria (Epicentre), followed by 100 bp paired-end, stranded library construction using 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: 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: 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: 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).

Mutagenesis:

Article Title: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: We used CancerScan™ to detect TP53 and PIK3CA mutation. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit and TruSeq Rapid SBS Kit (Illumina).

Isolation:

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: 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: 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: 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: Clinical implications of genomic profiles in metastatic breast cancer with a focus on TP53 and PIK3CA, the most frequently mutated genes
Article Snippet: After hybridization of the library with bait sequences for 27 hours, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were assessed. .. Sequencing of the exome library was performed using the 100-bp paired-end mode of the TruSeq Rapid PE ClusterKit 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: Recurrent mutations of MAPK pathway genes in multiple myeloma but not in amyloid light-chain amyloidosis
Article Snippet: After hybridization of the library with bait sequences for 27 hr, the captured library was purified and amplified with an index barcode tag, and the library's 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 the TruSeq Rapid SBS kit (Illumina).

Polymerase Chain Reaction:

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: 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) .

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: Regulation of tumour related genes by dynamic epigenetic alteration at enhancer regions in gastric epithelial cells infected by Epstein-Barr virus
Article Snippet: Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), following the manufacturer’s protocol. .. 500 platform using the TruSeq Rapid SBS Kit (Illumina) in 50-base single-end mode according to the manufacturer’s protocol.

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: 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).

Preserving:

Article Title: Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Article Snippet: For each sample, 20 µl total RNA was added to an RNAstable tube (Biomatrica), gently mixed with the preservation agent and left to air-dry in a biosafety cabinet for 48 h. Samples were shipped at ambient temperature to Macrogen (Geumcheon-gu, Seoul, Republic of Korea) for RNA-seq. .. Ribosomal RNA was removed by treatment with the Ribo-Zero rRNA removal kit for bacteria (Epicentre), followed by 100 bp paired-end, stranded library construction using the TruSeq rapid SBS Kit (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).

High Throughput Screening Assay:

Article Title: Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches
Article Snippet: A high-throughput 3′ digital gene expression RNA-sequencing (DGE-seq) protocol was performed as described previously [ ]. .. A library of 350–800 base pairs (bp) was run on an Illumina HiSeq 2500 using a TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

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).

Hood:

Article Title: Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung
Article Snippet: For each sample, 20 µl total RNA was added to an RNAstable tube (Biomatrica), gently mixed with the preservation agent and left to air-dry in a biosafety cabinet for 48 h. Samples were shipped at ambient temperature to Macrogen (Geumcheon-gu, Seoul, Republic of Korea) for RNA-seq. .. Ribosomal RNA was removed by treatment with the Ribo-Zero rRNA removal kit for bacteria (Epicentre), followed by 100 bp paired-end, stranded library construction using the TruSeq rapid SBS Kit (Illumina).

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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 49 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq rapid sbs kit hs
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