Sbs v3 chemistry

Manufactured by Illumina

Sourced in United States

The SBS v3 chemistry is a core component of Illumina's next-generation sequencing platform. It provides the fundamental chemical reactions and processes that enable the accurate and reliable detection of DNA sequences during the sequencing run.

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Lab products found in correlation

Hiseq 2000, by Illumina (1 mentions) Hiseq 2500, by Illumina (1 mentions)

Spelling variants of this product

V3 chemistry (30 citations) TruSeq SBS v3 chemistry (11 citations) TruSeq SBS Kit v3 chemistry (3 citations) TruSeq SBS Kit v3-HS chemistry (2 citations)

3 protocols using sbs v3 chemistry

RNA-seq Analysis of Breast Carcinomas

Cited 1 time

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RNA sequencing was performed using 16 ng of ribosomal-depleted RNA of 14 papillary carcinomas of the breast (three SF3B1 mutant and 11 SF3B1 wild-type) (Supplementary methods). Four indexed samples were pooled at equimolar concentrations and sequenced on a single lane of a HiSeq 2500 using SBS v3 chemistry (Illumina, San Diego, CA, USA) (2 × 76 cycles). Samples were aligned to the human genome (hg19 build 37) using TopHat version 2.0.8b. Raw counts of reads mapped to genes were calculated using HT-Seq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and used as input for differential exon usage analysis using DEXSeq [24 (link)], with an adjusted p-value cut-off of ≤0.1. FASTQ files from available TCGA RNA-sequencing data from SF3B1 K700E mutant (n = 8) and ER, PR, HER2 status, and PIK3CA and TP53 mutational status, and randomly matched controls (n = 16) were downloaded from the Cancer Genomics Hub (CGHub; https://cghub.ucsc.edu) and processed as above (TCGA project access number 6223).
Raw targeted re-sequencing and RNA-sequencing data have been deposited in the Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) and are available under accession numbers PRJNA234087 and PRJNA229096.

Maguire S.L., Leonidou A., Wai P., Marchiò C., Ng C.K., Sapino A., Salomon A.V., Reis-Filho J.S., Weigelt B, & Natrajan R.C. (2014). SF3B1 mutations constitute a novel therapeutic target in breast cancer. The Journal of Pathology, 235(4), 571-580.

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Whole Exome Sequencing of Genomic DNA

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Blood was obtained via venipuncture from all 142 participants and genomic DNA was extracted from whole blood. We used 1 μg of genomic DNA to construct whole genome libraries. Multiplexed genomic libraries of four different individuals were subjected to whole exome capture using NimbleGen SeqCap version 3. Exome libraries were sequenced with paired-end 100 bp reads on the Illumina HiSeq2000 (San Diego, CA, USA) using Illumina SBS V3 chemistry. This approach captures 62 Mb of the genomic sequence comprising exonic variants (variants in protein-coding portion), ncRNA variants (variants in noncoding RNAs), untranslated region (UTR) or intronic variants (variants in UTRs and intron regions) and intergenic variants (variants between mRNA transcripts of two genes).

An J.Y., Cristino A.S., Zhao Q., Edson J., Williams S.M., Ravine D., Wray J., Marshall V.M., Hunt A., Whitehouse A.J, & Claudianos C. (2014). Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach. Translational Psychiatry, 4(6), e394-.

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Differential exon usage in breast papillary carcinoma

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RNA-sequencing was performed using 16ng of ribosomal-depleted RNA of 14 papillary carcinomas of the breast (3 SF3B1 mutant and 11 SF3B1 wild-type) (Supplementary Methods). Four indexed samples were pooled at equimolar concentrations and sequenced on a single lane of a HiSeq 2500 using SBS v3 chemistry (Illumina) (2 × 76 cycles). Samples were aligned to the human genome (hg19 build 37) using TopHat version 2.0.8b. Raw counts of reads mapped to genes were calculated using HT-Seq (http://www-huber.embl.de) and used as input for differential exon usage analysis using DEXSeq [24 (link)], with an adjusted P-value cut-off of ≤0.1. FASTQ files from available TCGA RNA-sequencing data from SF3B1 K700E mutant (n=8) and ER, PR, HER2 status, PIK3CA and TP53 mutational status, and randomly matched controls (n=16) were downloaded from the Cancer Genomics Hub (CGHub, https://cghub.ucsc.edu) and processed as above (TCGA project access number 6223).

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