|
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 |