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Sample GSM2199390 Query DataSets for GSM2199390
Status Public on Aug 04, 2016
Title aTr_LCMV_rep2 (Sample 27)
Sample type SRA
 
Source name aTr_LCMV
Organism Mus musculus
Characteristics tissue: Spleen
cell type: Activated Treg cells
source: Foxp3-GFP-DTR_CD4CreER_R26tdTomato
activating stimulus: LCMV-infection
days post-stimulus: 11 days
Extracted molecule total RNA
Extraction protocol Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description tdTomato+ Foxp3+ CD4 T cells were isolated from animals treated with tamoxifen and infected with LCMV
Data processing Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples
 
Submission date Jun 13, 2016
Last update date May 15, 2019
Contact name Hyein Sophia Cho
E-mail(s) [email protected]
Organization name Memorial Sloan Kettering Cancer Center
Department Developmental Biology
Street address 430 E 67th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL13112
Series (1)
GSE83315 Memory of inflammation in regulatory T cells
Relations
BioSample SAMN05240624
SRA SRX1842254

Supplementary file Size Download File type/resource
GSM2199390_Sample_LCMV_aTr2.rmdup.bam-genes.txt.gz 79.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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