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Sample GSM2199367 Query DataSets for GSM2199367
Status Public on Aug 04, 2016
Title aTr_rep1 (Sample 4)
Sample type SRA
 
Source name aTr
Organism Mus musculus
Characteristics tissue: Spleen and peripheral lymph nodes
cell type: Activated Treg cells
source: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow
activating stimulus: Transient Treg cell depletion
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 YFP+ GFP+ Treg cells were isolated from animals treated with tamoxifen and diphtheria toxin
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 SAMN05240601
SRA SRX1842231

Supplementary file Size Download File type/resource
GSM2199367_Sample_aTreg_rep1-genes.htseq.txt.gz 78.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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