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Sample GSM2254213 Query DataSets for GSM2254213
Status Public on Aug 30, 2016
Title WT.Treg_RNAseq.4
Sample type SRA
Source name T-reg cells
Organism Mus musculus
Characteristics genotype/variation: WildType
mouse group: 2
strain: C57BL/6J
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
Libraries were prepared with Illumina TruSeq Stranded mRNA sample kits using indexed adaptors (Illumina).
Pooled libraries were subjected to 75 bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000). Targeted sequencing depth was 30 million paired-end reads per sample.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Mouse Group 2; Wild Type Treg Cells
Data processing Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
RNA sequencing reads were mapped with the TopHat 2 aligner using the default parameters to the UCSC mm10 mouse reference genome.
Reads were examined for quality control and quantified using FeatureCounts.
Raw counts were normalized taking into account library sizes, filtering out genes with ~0 expression (remaining gene, n=13700), and applying the variance-stabilizing transformation using the DESeq2 software package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and normalized (varriance stabilized) text files as csv.
Submission date Jul 27, 2016
Last update date May 15, 2019
Contact name Jeffrey C Rathmell
Organization name Vanderbilt University Medical Center
Street address 1161 21st Avenue South, A-5301 MCN
City Nashville
State/province Tennessee
ZIP/Postal code 37232-2363
Country USA
Platform ID GPL21493
Series (1)
GSE84919 Gene expression of Glut1 transgenic and control iTreg
BioSample SAMN05449635
SRA SRX1981241

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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