NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM640690 Query DataSets for GSM640690
Status Public on Jan 25, 2011
Title hESC_Input_XL_ChIP-Seq
Sample type SRA
 
Source name Input DNA: H9 human embryonic stem cell (hESC)
Organism Homo sapiens
Characteristics cell line: H9 hESC
developmental stage: embryonic stem cell
chip antibody: none
Growth protocol H9 hESCs (WiCell, Madison, WI) were cultured in CDM with 10 ng/ml Activin A and 12 ng/ml FGF2 as described previously (Brons et al., Nature, 2007, 448(7150):191-5). hESCs were induced to differentiate into endoderm using CDM-PVA + 100 ng/ml Activin + 10 ng/ml BMP4 + 20 ng/ml FGF2 + 10 uM LY294002 (Promega) (Touboul et al., Hepatology, 2010, 51(5):1754-65).
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared using the Solexa ChIP-seq DNA sample prep kit (IP102-1001). After amplification, DNA fragments of between 180 to 400bp were gel extracted and the purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Input control for ChIP-Seq: DNA cross linked with formaldehyde plus extra chemical linkers.
One rep: Control_s_1
Data processing Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained. Reads were filtered for overlap with UCSC hg18 RepeatMasker.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/) as described in (Teo et al. Genes Dev, 2010, In Press).
 
Submission date Dec 16, 2010
Last update date May 15, 2019
Contact name Matthew Trotter
E-mail(s) mwbt2@cam.ac.uk
Organization name University of Cambridge
Department Department of Surgery
Lab Laboratory for Regenerative Medicine
Street address West Forvie Building, Forvie Site, Robinson Way
City Cambridge
ZIP/Postal code CB2 0SZ
Country United Kingdom
 
Platform ID GPL9115
Series (1)
GSE26097 Pluripotency Factors Regulate Definitive Endoderm Specification through Eomesodermin
Relations
SRA SRX035158
BioSample SAMN00149671

Supplementary file Size Download File type/resource
GSM640690_Control_XL_2M_RM.bed.gz 39.7 Mb (ftp)(http) BED
GSM640690_s_1_eland_extended.txt.gz 469.2 Mb (ftp)(http) TXT
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