|
| Status |
Public on May 20, 2009 |
| Title |
Bmi1 KO MEF uH2A |
| Sample type |
SRA |
| |
|
| Source name |
Bmi1 KO C57BL/6 MEF cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Bmi1 KO
antibody: anti-uH2A(E6C5)
|
| Treatment protocol |
Cells were grown under standard conditions and were not subjected to further treatment before harvesting for ChIP-Seq experiments
|
| Growth protocol |
TBX2 immortalized MEF cells were cultured in Dulbecco’s modified eagle medium (Gibco, Cat# 10829) supplemented with 10% FBS and were maintained at 37°C, 7% carbon dioxide, and passaged onto new plates following trypsin dissociation ever 3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For chromatin immunoprecipitation (ChIP) using a anti-uH2A(E6C5) (Cao et al., 2005, Mol Cell, PMID: 16359901), the formaldehyde cross-linked cells were sonicated and subjected to MNase digestion to obtain DNA fragments ranging in size from ~200-300 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP with anti-uH2A E6C5
|
| Data processing |
Sequenced 25-bp reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. Reads that mapped to unique genomic locations with at most 2 mismatches were processed further to using the TIROE algorithm to identify genomic regions specifically enriched for mapped reads in the WT MEF sample 1 as compared to Bmi1 KO MEF Sample 2 with p-value threshold E-5.
|
| |
|
| Submission date |
Apr 29, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Raja Jothi |
| E-mail(s) |
jothi@mail.nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Environmental Health Sciences
|
| Lab |
Systems Biology
|
| Street address |
111 TW Alexander Drive; A314
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE15896 |
Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes. |
| GSE15909 |
Gene expression and UH2A ChIP-Seq binding analysis in Bmi1 knock-out and wild type MEFs |
|
| Relations |
| SRA |
SRX005251 |
| BioSample |
SAMN02197758 |
| Named Annotation |
GSM399091_mm8-Bmi1-ko-H2Aub.bed.gz |
