|
| Status |
Public on Jun 15, 2012 |
| Title |
RA 2h ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
murine embryonic stem cells grown as embryoid bodies for 4 days and treated 2 hours with 5 micromolar all trans retinoic acid
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ES cells grown as embryoid bodies
treatment: all trans retinoic acid
time: 2 h
chip antibody: anti-RAR
chip antibody manufacturer: Santa Cruz
chip antibody catalog #: sc-773
|
| Treatment protocol |
Embryoid bodies were treated with all trans retinoic acid dissolved in ethanol. Celle were fixed with 0.4 % formaldehyde for 10 minutes before scraping and sonnication.
|
| Growth protocol |
Murine ES cells were grwon under standard conditions in the presence of LIF and inactivated fibroblast feeder cells. Cells were passaged three times in absence of feeder cells and then transfered to bacterial dishes to initiate embryoid body formation. Embryoid bodies were grwon for 4 days before RA treatement
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, lysates were clarified from sonicated nuclei and RAR-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. For RNA-seq, total RNA was isolated with trizol and mRNA-seq libraries were prepared after selection of the polyA containing fraction using the standard Illumina protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
nuclear chromatin
|
| Data processing |
Counts: Sequence reads were obtained and mapped to the Mouse (July, 2007) genomes mm9 using the Illumina Genome Analyzer Pipeline and Bowtie aligner. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
RA_2h_ChIPSeq_reads.bed: mm9
|
| |
|
| Submission date |
Feb 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao YE |
| Organization name |
IGBMC (CNRS/INSERM/UDS)
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE35599 |
Relocalization of retinoic acid receptors from non-canonical to canonical spaced binding elements during embryoid body differentiation |
|
| Relations |
| SRA |
SRX118692 |
| BioSample |
SAMN00783701 |
