|
Status |
Public on May 29, 2018 |
Title |
Sample014_Systemic JIA |
Sample type |
SRA |
|
|
Source name |
Whole Blood
|
Organism |
Homo sapiens |
Characteristics |
gender: Female age at diagnosis: 1.5 ancestry: Black disease state (diagnosis): Systemic JIA tissue: Whole Blood
|
Extracted molecule |
total RNA |
Extraction protocol |
Blood was collected via Tempus Tube and RNA was extracted with Tempus Spin RNA isolation kit. RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq stranded mRNA library kit and sequenced on the Illumina HiSeq Rapid Run with paired-end 100-bp reads (Illumina, San Diego, CA).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Reads were mapped to the human genome (hg19) with TopHat 2.0.13 using default parameters, aligned reads were transformed with SAMtools to quantify number of reads at the gene level with HTSeq-0.6.1 using default “union” mode. counts were transformed to RPKM to follow GTEx QC guidelines, retaining 11,924 genes with RPKM>1 and >6 read counts in at least 10 individuals finally, original raw counts of the retained genes were normalized using TMM normalization with edgeR Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text file include raw counts or normalized read counts at the gene level for each sample
|
|
|
Submission date |
Mar 20, 2018 |
Last update date |
May 29, 2018 |
Contact name |
Angela Mo |
E-mail(s) |
amo3@gatech.edu
|
Organization name |
Georgia Institute of Technology
|
Department |
School of Biological Sciences
|
Street address |
950 Atlantic Drive
|
City |
Atlanta |
State/province |
GA |
ZIP/Postal code |
30332 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE112057 |
Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease |
|
Relations |
BioSample |
SAMN08742037 |
SRA |
SRX3823015 |