|
| Status |
Public on Sep 16, 2015 |
| Title |
input_KO_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
MEFs cells knockout MED23
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast
genotype/variation: MED23 knockout
|
| Growth protocol |
MEFs cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (vol/vol) FBS (Hyclone)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysates were sonicated and immunoprecipitated DNA-protein complex using antibody (Millipore, Cat. #05-1312, Lot #DAM1567819); Pol II (N20, Santa Cruz, Cat. sc-899).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
CASAVA version 1.6 used for base-calling
Sequencing reads were alligned to mouse genome by Bowtie version 0.12. 8 and parameters are followings:-v1, --best, --strata, -k2, -m1
Peak calling was performed independently for each sample using MACS software version 1.4.2 by p-value threshold of 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: wiggle files were generated using MACS version 1.4.2. Scores represent fragments pileup at every 10 bps of ChIP-seq.
|
| |
|
| Submission date |
Jul 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gang Wang |
| Organization name |
Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
| Department |
Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology,
|
| Lab |
Gang Wang's Lab
|
| Street address |
Yueyang Road 320
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE59518 |
The Mediator complex subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination |
|
| Relations |
| BioSample |
SAMN02921335 |
| SRA |
SRX655693 |
