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Sample GSM2199396 Query DataSets for GSM2199396
Status Public on Aug 04, 2016
Title rTr_ATAC_rep2 (Sample 33)
Sample type SRA
 
Source name rTr_ATAC
Organism Mus musculus
Characteristics tissue: Spleen and peripheral lymph nodes
cell type: Resting Treg cells
source: mixed bone marrow chimeras generated with 90% Foxp3-GFP-DTR /10% Foxp3-GFP-CRE-ERT2XR26Y bone marrow
activating stimulus: none
days post-stimulus: NA
Extracted molecule genomic DNA
Extraction protocol FACS-sorted cell populations (5x104 cells) were lysed and accessible chromatin was transposed using Nextera Tn5 transposase. Transposed DNA fragments were isolated using Qiagen MinElute kit and amplified 5-10 cycles using Nextera PCR primers. ATAC-seq libraries were sequenced on Illumina Hiseq.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Bulk GFP+ Treg cells were isolated from animals treated with tamoxifen only
Data processing Library strategy: ATAC-seq
Sequences mapped using bowtie2 2.2.0
Peak was called with macs2 with p-value cutoff of 0.01
Peaks below the IDR cutoff of 0.005 were selected
The union of ATAC-seq peaks were found, and reads overlapping this peak atlas were counted.
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 SAMN05240630
SRA SRX1842260

Supplementary file Size Download File type/resource
GSM2199396_r2-countsatatacseqpeaks.txt.gz 632.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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