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Sample GSM999187 Query DataSets for GSM999187
Status Public on Sep 28, 2012
Title CD4 Ets1 ChIP
Sample type SRA
Source name CD4 Ets1 ChIP
Organism Mus musculus
Characteristics cell type: CD4+ Foxp3-negative T cells
cell source: Primary Mouse T cells isolated ex-vivo and sorted
Treatment protocol Ets1 antibody; Santa Cruz Biotechnologies sc-350-X Lot# J1309
Extracted molecule genomic DNA
Extraction protocol Cells were harvested from mice that were approximately 8 weeks old. Lymphnodes and spleen were extracted and sorted based on GFP (Foxp3). Cells were fixed with formaldehyde, nuclei were extracted and sonicated. Antibodies were incubated with sonicated chromatin. Standard illumina kit was used for library construction.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description CD4 Ets1 ChIP
Data processing Base calling was performed using Illumina software pipeline (Genome Analyzer)
Align to the mouse genome (mm9) using bowtie (version 0.12.7) allowing 1 mismatch and reporting only uniquely aligning hits.
Peak calling was perfomed using SPP and MACS. Number of peaks was estimated as described in our manuscript.
Genome_build: mm9
Submission date Sep 07, 2012
Last update date May 15, 2019
Contact name Aaron Arvey
Organization name Memorial Sloan-Kettering Cancer Center
Street address 415 E 68th St ZRC 1441
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL13112
Series (2)
GSE40684 Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [ChIP-Seq]
GSE40686 Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification
SRA SRX184868
BioSample SAMN01163375

Supplementary file Size Download File type/resource
GSM999187_Sample_CD4_Ets1.bowtie.align.out.binding.positions.txt.gz 5.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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