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Sample GSM871397 Query DataSets for GSM871397
Status Public on Jun 15, 2012
Title RA 24h RNASeq
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
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 total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description total RNA
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 (
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
SRA SRX118694
BioSample SAMN00783703

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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