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Sample GSM2430374 Query DataSets for GSM2430374
Status Public on Apr 11, 2017
Title Irritable bowel syndrome
Sample type SRA
Source name peripheral whole blood draw
Organism Homo sapiens
Characteristics type: Irritable bowel syndrome
Extracted molecule total RNA
Extraction protocol Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
Libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Data processing Illumina Casava1.9 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, FPKM table
Submission date Dec 15, 2016
Last update date May 15, 2019
Contact name Charles F Spurlock III
Phone 6153432363
Organization name Vanderbilt University School of Medicine
Department Medicine
Lab T3113
Street address 1161 21st Avenue South
City Nashville
State/province Tennessee
ZIP/Postal code 37232
Country USA
Platform ID GPL21290
Series (1)
GSE92472 Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants
BioSample SAMN06146241
SRA SRX2430564

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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