|
| Status |
Public on Jun 19, 2017 |
| Title |
rheumatoid arthritis tissue 17 |
| Sample type |
SRA |
| |
|
| Source name |
synovial biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: F
age: 55
disease: Rheumatoid arthritis (early)
acpa positivity: Positive
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from RA synovial samples and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer
Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina. Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cells. Raw read quality was evaluated using FastQC.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were trimmed for adaptors and sequence quality. The average number of clusters (post-trimming) per sample was 89 million.
Trimmed reads were aligned to human b37.3 reference genome using the STAR v2.4 aligner (Dobin et al., 2013).
Aligned reads were quantified using RSEM v1.2.14 algorithm (Li and Dewey, 2011) with UCSC transcriptome model (accessed on 03/17/2014) that included lincRNAs from Ensembl v75. This transcriptome model has a total of 34495 genes and 88933 isoforms
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features
|
| |
|
| Submission date |
Nov 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alice Walsh |
| E-mail(s) |
awalsh17@its.jnj.com
|
| Organization name |
Janssen R&D
|
| Department |
Immunology
|
| Street address |
Welsh & McKean Roads
|
| City |
Spring House |
| State/province |
PA |
| ZIP/Postal code |
19477 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE89408 |
RNAseq study of synovial biopsies |
|
| Relations |
| BioSample |
SAMN05963914 |
| SRA |
SRX2316125 |
