|
| Status |
Public on Jan 26, 2016 |
| Title |
Smarca4 ChIP-Seq replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 46C (129/Ola strain)
cell line: TAP-tag introduced by homologous recombination at the gene encoding Smarca4
chip antibodies: sequential ChIP whith HA and FLAG antibodies
|
| Treatment protocol |
none
|
| 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 |
Formaldehyde-fixed chromatin was digested by MNase to release individual nucleosomes
Libraries were prepared according to the Illumina ChIP-seq protocol. Following end-repair and adapter ligation, fragments were size-selected on an agarose gel to purify genomic DNA fragments between 140 and 180 bp. Purified fragments were next amplified before clustering and single-read sequencing
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity/low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -a -m1 --best --strata -v2 p3
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
|
| |
|
| Submission date |
Jan 09, 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 |
GPL11002 |
| Series (1) |
| GSE64825 |
Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN03280142 |
| SRA |
SRX835498 |
