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Sample GSM2629900 Query DataSets for GSM2629900
Status Public on Nov 16, 2018
Sample type SRA
Source name CCP-specific B cells
Organism Homo sapiens
Characteristics sample preparation: Ex vivo
cell type: B cells
tissue: Blood
Extracted molecule total RNA
Extraction protocol Antigen-specific B cells were sorted from PBMCs from patients' blood directly into lysis buffer and RNA was isolated using RNA isolation kit (Macherey-Nagel, RNA-XS).
cDNA libraries were synthesized using the commercially available SMART-Seq Ultra Low Input RNA kit (Clontech), cDNA libraries were first tagmented and then barcoded by indexing primers using the Nextra XT kit (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Quality control of the sequencing data was performed by using Cutadapt (1.8.3) to remove the adapter sequences from the 3’ end, followed by trimming of the first 12 bases of all reads at 5’ end to address the non-uniform distribution caused either by biased selection of reads or contamination of other sequences.
Reads shorter than 20bp were then dropped to avoid potential mapping to multiple locations on the reference genome.
Transcripts were aligned to the human reference genome UCSC hg19 using TopHat2 (v2.1.0). The mapped genes were annotated using R package “GenomicAlignments” (1.0.6) and gene annotation information in R package “TxDb.Hsapiens.UCSC.hg19.knownGene” (2.14.0).
Differentially expressed genes (DEGs) were identified using DEseq2 (1.4.5) tool that tests for differential gene expression based on a model using the negative binomial distribution.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with normalized count of gene transcripts from each sample
Submission date May 17, 2017
Last update date May 15, 2019
Contact name Navin Varadarajan
Organization name University of Houston
Department Chemical and Biomolecular Engineering
Street address 4726 Calhoun Rd
City Houston
State/province Texas
ZIP/Postal code 77204
Country USA
Platform ID GPL21290
Series (1)
GSE99006 Whole transcriptome profile of citrulline-specific B cells from patients with rheumatoid arthritis
BioSample SAMN07137237
SRA SRX2831276

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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