|
| Status |
Public on Feb 03, 2017 |
| Title |
Pool2_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
3T3-L1 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
chip antibody: PPARG (Cell Signaling Technologies SC-7196X)
molecule subtype: genomic DNA
|
| Treatment protocol |
none
|
| Growth protocol |
3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days after confluence, the cells were induced with DMEM supplemented with 10% FBS, 1uM dexamethasone, 1.7uM insulin, and 0.5mM 3-isobutyl-1-methylxanthine (IBMX). 48h later, the medium was replaced with DMEM supplemented with 10% FBS and the cells were fed every two days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq libraries were prepared as described by Mikkelsen et al. (Nature 2007; 448(7153):553-60; PMID: 17603471)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Chromatin IP against PPARG
processed data file: Pool2_ChIP.counts.txt
|
| Data processing |
Reads were mapped to plasmids using BWA 0.7.12 (Li and Durbin, 2009) with default parameters. Reads with MAPQ<20 were removed.
Total reads in ChIP and WCE libraries corresponding to each oligo
Genome_build: mm9
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sharon R Grossman |
| E-mail(s) |
grossman@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE84888 |
Distinct roles for motif affinity, chromatin state, and co-regulatory motifs in PPARĪ³ binding and enhancer activity |
|
| Relations |
| BioSample |
SAMN05447719 |
| SRA |
SRX1979663 |
