|
| Status |
Public on Nov 04, 2011 |
| Title |
Cdk9_0hr_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
KH2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 (female) x 129/S (male)
cell type: mES
passages: passage 10-18
chip antibody: His tag Cdk9(amino acids 204-372)
|
| Treatment protocol |
For RA induction, mouse ES cells were treated with 0.3 uM of all-trans retinoic acid for 6 hours. For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoy’s 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.
|
| Growth protocol |
Mouse embryonic stem cells (KH2) were cultured under feeder-free medium ESGRO (Millipore). HCT-116 cells were grown in McCoy’s 5A medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed according to previously described protocols (Wang et al. 2009 [MCB]). Briefly, ES cells were cross-linked by 1% formaldehyde and sonicated. 10 ug of antibodies were used in the ChIP assays. The ChIP Libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols. Antibodies for Pol II are from Covance, 8WG16, catalog #MMS-126R. Other antibodies were sourced from the original work of Lin et al. 2010 (Mol. Cell)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against Cdk9
|
| Data processing |
Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the mouse genome (NCBI build 37, UCSC mm9) or the human genome (UCSC hg19) using the bowtie (Langmead et al., 2009) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained.
Peaks: Enriched regions of ChIP-seq signal were determined by the ‘MACS’ (Zhang et al.,2008) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for mouse and human datasets, and the p-value cutoff was set to 1.00e-08 or FDR <= 1%, and a foldchange greater than five.
|
| |
|
| Submission date |
Nov 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE30267 |
Super Elongation Complex (SEC) and global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. |
|
| Relations |
| SRA |
SRX104410 |
| BioSample |
SAMN00750187 |
