|
| Status |
Public on Jun 04, 2012 |
| Title |
H3K4me2 ChIP-seq in P19.6 cells |
| Sample type |
SRA |
| |
|
| Source name |
P19.6_H3K4me2 ChIP-seq
|
| Organism |
Mus musculus |
| Characteristics |
cell line: P19.6
cell type: embryonal carcinoma cells
chip antibody: Anti-H3K4me2
chip antibody vendor: Millipore
chip antibody cat. #: 05-1338
chip antibody lot #: DAM1570816
|
| Treatment protocol |
P19.6 cells were differentiated with 1 µM all-trans retinoic acid (RA) for 48 hours.
|
| Growth protocol |
P19.6 mouse embryonal carcinoma cells were grown in high glucose Dulbeccos’ Modified Eagle’s Medium (DMEM) containing 10% fetal calf serum (GIBCO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions by IGBMC sequencing facility (Strasbourg, France)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads were mapped to the reference genome (mouse mm8) by Bowtie (Langmead et al. Genome Biol. 2009) using parameters -l 28 -n 1 -m 1 --best --strata.
Mapped reads were processed by MACS algorithm (Model-based Analysis of ChIP-Seq) (Zhang Y. et al. Genome Biol. 2008).
Genome_build: mm8
Supplementary_files_format_and_content: wig files were generated using macs 1.4.
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Aurelien Serandour |
| E-mail(s) |
aurelien.serandour@cruk.cam.ac.uk
|
| Phone |
00441223769723
|
| Organization name |
Université de Rennes 1
|
| Department |
UMR CNRS 6290
|
| Lab |
Equipe SP@RTE
|
| Street address |
Bâtiment 13, Campus de Beaulieu
|
| City |
Rennes |
| ZIP/Postal code |
35042 |
| Country |
France |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE27436 |
Dynamic hydroxymethylation of DNA marks differentiation-driven enhancers |
| GSE33067 |
Whole-genome mapping of MEIS1, TET1, H3K4me2 and H3K27ac in P19.6 mouse embryonal carcinoma cells and P19.6 cells treated for 48 hours with all-trans retinoic acid |
|
| Relations |
| SRA |
SRX151237 |
| BioSample |
SAMN01001974 |
| Named Annotation |
GSM941682_P19_-RA_H3K4me2_mm8.wig.gz |
