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Sample GSM3056569 Query DataSets for GSM3056569
Status Public on May 29, 2018
Title Sample176_Control
Sample type SRA
 
Source name Whole Blood
Organism Homo sapiens
Characteristics gender: NA
age at diagnosis: NA
ancestry: NA
disease state (diagnosis): Control
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 SAMN08741789
SRA SRX3823177

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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