|
| Status |
Public on Nov 16, 2018 |
| Title |
RA1-CCPPOS |
| 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 |
|
| Relations |
| BioSample |
SAMN07137239 |
| SRA |
SRX2831274 |
