NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM871396 Query DataSets for GSM871396
Status Public on Jun 15, 2012
Title RA 24h ChIPSeq
Sample type SRA
 
Source name murine embryonic stem cells grown as embryoid bodies for 4 days and treated 24 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: 24 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_24h_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 SRX118693
BioSample SAMN00783702

Supplementary file Size Download File type/resource
GSM871396_RA_24h_ChIPSeq_reads.bed.gz 185.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap