GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM783881 Query DataSets for GSM783881
Status Public on Oct 13, 2011
Title H3K27me3 forebrain ChIPSeq
Sample type SRA
Source name Forebrain cells
Organism Mus musculus
Characteristics strain: B6CBAF1/J
age: E10.5
cell type: forebrain cells
chip antibody: H3K27me3
Treatment protocol Tissue samples were isolated in PBS supplemented with 10% Fetal Calf Serum and made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Nuclei were sonicated to generate fragments with average length around 300 bp.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against H3K27me3
Data processing Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.5 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Duplicated reads (reads mapping at exactly the same genomic position in the same orientation) were removed as probable PCR artifacts. Genome coverage densities were calculated for each strand separately, then shifted downstream by 70 bp, averaged and normalized by the total number of mapped reads (times 10^-7). Enriched regions were detected using MACS version 1.4.0beta (Zhang et al., 2008) and selected for a p-value<0.001 and an FDR<0.05. Signal on chromosomes not containing Hox clusters was removed.
Submission date Aug 22, 2011
Last update date May 15, 2019
Contact name Marion LELEU
Organization name EPFL
Department School of Life Sciences
Lab Laboratory of developmental genomics
Street address EPFL-SV-ISREC-UPDUB- Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platform ID GPL11002
Series (1)
GSE31570 The Dynamic Architecture of Hox Gene Clusters
SRA SRX093314
BioSample SAMN00714234

Supplementary file Size Download File type/resource 29.5 Mb (ftp)(http) BW
GSM783881_FB_H3K27_peaks_fdr5.bed.gz 100.9 Kb (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