|
| Status |
Public on Sep 28, 2012 |
| Title |
CD4 Elf1 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
CD4 Elf1 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 |
Elf1 antibody; Santa Cruz Biotechnologies sc-631-X Lot# G2406
|
| 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 Elf1 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 |
| E-mail(s) |
aarvey@cbio.mskcc.org
|
| 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 |
|
| Relations |
| SRA |
SRX184866 |
| BioSample |
SAMN01163373 |
