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Sample GSM539552 Query DataSets for GSM539552
Status Public on Aug 24, 2011
Title WCE - BGO3
Sample type SRA
 
Source name Embryonic stem cells
Organism Homo sapiens
Characteristics cell type: BGO3 (feeder free)
chip antibody: None (WCE)
antibody vendor: n/a
antibody catalog number: n/a
Growth protocol hES cells were grown in mTESR media (Stem Cell Technologies) on plates coated with matrigel (BD Biosciences) in the absence of feeder cells.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description 05082009_42750AAXX_B2
WCE sequence for BGO3 FF cells
Data processing Images analysis and base calling was done using the solexa pipeline.
Reads aligned to mouse NCBI build 36 (mm8 for mouse samples and hg18 for human) using BOWTIE.
For ChIP-Seq, sequences from all lanes were extended 200bp downstream (with respect to strand), and allocated into 25 bp bins. Reads from replicates were merged and genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9. Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) or IgG IP's from matched cell samples (>5X normalized enrichment across the entire region). WIG tracks show bins with at least 2 counts in the respective dataset (after replicate merging, where appropriate).
 
Submission date Apr 30, 2010
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9115
Series (2)
GSE21614 Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity: ChIP-Seq
GSE21621 Cell-Type-Specific TGF-beta Signaling is Targeted to Genes that Control Cell Identity
Relations
SRA SRX026253
BioSample SAMN00014825

Supplementary file Size Download File type/resource
GSM539552_05082009_42750AAXX_B2.ylf.txt.gz 33.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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