|
| Status |
Public on May 10, 2017 |
| Title |
JIA36 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
mtx response status: responder
cohort: 2
condition: juvenile idiopathic arthritis (JIA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNeasy columns (Qiagen) or mirVana miRNA Isolation (Ambion) protocols, respectively for samples stored in TRIzol (cohort 1) or RNAlater (cohort 2).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
JIA patient prior to MTX treatment
|
| Data processing |
fastq seqences aligned to hg19 using Tophat
number of reads calculated for each Entrez gene
differential expression analysis performed using edgeR
log-2 transformed rpkm (reads per kilobase of transcript per million reads mapped) computed and adjusted for batch difference between cohorts using ComBat
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited log2rpkm, with genes in rows and samples in columns
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Medvedovic |
| Organization name |
University of Cincinnati
|
| Department |
Department of Environmental Health
|
| Lab |
Laboratory for Statistical Genomics and Systems Biology
|
| Street address |
3223 Eden Av. ML 56
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267-0056 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE81259 |
Transcriptional profiling reveals monocyte signature associated with JIA patient poor response to methotrexate |
|
| Relations |
| Reanalyzed by |
GSE122515 |
| BioSample |
SAMN04966103 |
| SRA |
SRX1753640 |
