|
| Status |
Public on Feb 10, 2012 |
| Title |
Runx1_induced_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Runx1_induced_ChIPseq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: L8057
|
| Treatment protocol |
For induced L8057 cells, 50 nM TPA was added to induced maturation of the cells for 72 hrs. L8057 cells and primary thymocytes were fixed with formaldehyde before sonicated for ChIP.
|
| Growth protocol |
L8057 cells were grown in 38.5% IMDM + 38.5% RPMI + 20% FCS + %2 Pen/strep + 1% L-Glutamine,
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The purified DNA was prepared for sequencing on a Beckman Coulter SPRI-TE following manufacturer’s instructions. The seq-prepped DNA was PCR amplified using Illumina primers for 18 cycles. Samples were sequenced on either the Illumina Genome Analyzer II or Illumina Hi-Seq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
maturation was induced by adding 50 nM (final concentration) 12-O- tetradecanoylphorbol-13-acetate (TPA) to the medium for 3 days
|
| Data processing |
Alignment: Raw ChIP-Seq data were processed using the Illumina software pipeline. Only ChIP-Seq reads that aligned to exactly one location in the reference mouse genome were retained (UCSC, mm9)
Peaks:The MACS algorithm (Zhang et al., 200b) was used to identify bound regions by comparing the enrichment of the IP sample against a control IgG IP for background correction. MACS version 1.4.0rc2 was run with all parameters at their default settings.
|
| |
|
| Submission date |
Nov 13, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tali Mazor |
| Organization name |
MIT
|
| Street address |
77 Massachusetts Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE33653 |
Direct Recruitment of Polycomb Repressive Complex 1 (PRC1) to Chromatin by Core Binding Transcription Factors (ChIP-Seq) |
| GSE33660 |
Direct Recruitment of Polycomb Repressive Complex 1 (PRC1) to Chromatin by Core Binding Transcription Factors |
|
| Relations |
| SRA |
SRX105446 |
| BioSample |
SAMN00752603 |
| Named Annotation |
GSM832311_Runx1_induced_1.bed.gz |
| Named Annotation |
GSM832311_Runx1_induced_peaks.bed.gz |
| Named Annotation |
GSM832311_Runx1_induced_2.bed.gz |
