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Sample GSM747546 Query DataSets for GSM747546
Status Public on Dec 09, 2011
Title ES_Input_ChIPseq_rep2
Sample type SRA
Source name ES_Input_ChIPseq
Organism Mus musculus
Characteristics strain: Mixed (129-C57Bl/6)
cell type: Embryonic stem cells
genotype/variation: wild type
Growth protocol Wild-type embryonic stem cells (129-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation (ChIP) assay for CTCF was performed according to the Upstate protocol. ChIP assay for REST was performed as previously described (Koch et al., 2007). ChIP experiments for Pax6, PolII and monomethylated H3K4 (H3K4me1) were performed as previously described (Weber et al., 2007). The antibodies used were: anti-monomethyl-H3K4(Abcam #ab8895), anti-CTCF(SantaCruz #15914), anti-PolII(), anti-REST (Santa Cruz #H-290)., anti-Pax6(Covance PRB-278P). ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/80 of ChIP or 20ng of input chromatin per PCR reaction. H3K4me1, CTCF, PolII and REST ChIP-seq libraries for Illumina sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols. Pax6 ChIP samples were amplified using the WGA2 kit (Sigma) and hybridized to a custom tiling microarray (NimbleGen Systems Inc.).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Input chromatin
Data processing 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Submission date Jun 24, 2011
Last update date May 15, 2019
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL11002
Series (2)
GSE30203 DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP-seq].
GSE30206 DNA binding factors shape the mouse methylome at distal regulatory regions.
SRA SRX080179
BioSample SAMN00631228

Supplementary file Size Download File type/resource
GSM747546_ChIPseq_Input_ES_rep2.wig.gz 27.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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