|
| Status |
Public on Jan 26, 2016 |
| Title |
Brg1 knockdown pol II ChIP-exo replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Brg1 knockdown pol II ChIP-exo, ESC
|
| Organism |
Mus musculus |
| Characteristics |
strain: 46C (129/Ola strain)
cell line: ESC line 46C
transfection: shRNA vector targeting Brg1, replicate 2
chip antibody: Pol II Antibody (N-20) (Santa Cruz Biotechnology, catalog# sc-899, lot# A2014)
|
| Treatment protocol |
described in the SAMPLES section (experimental conditions)
|
| Growth protocol |
Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and leukemia inhibitory factor (LIF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-exo using an antibody anti-RNA polymerase II: The immunoprecipitation step was performed using antibodies against Pol II (sc-899, Santa Cruz Biotechnology) attached to magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads.
After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR-amplified and gel-purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
library strategy: ChIP-exo
|
| Data processing |
Basecalls was performed using Bcl2FastQ version 2.16.0. Sequenced reads were masked for low-quality sequence, then mapped to mm9 whole genome using bwa mem 0.7.9a with the default parameters
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program
|
| |
|
| Submission date |
Nov 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthieu GERARD |
| E-mail(s) |
matthieu.gerard@cea.fr
|
| Organization name |
CEA
|
| Department |
I2BC
|
| Lab |
Mammalian Epigenomics
|
| Street address |
SBIGeM bldg 142
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91191 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE64825 |
Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN04271231 |
| SRA |
SRX1433584 |
