NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM743038 Query DataSets for GSM743038
Status Public on Nov 02, 2012
Title Input DNA
Sample type SRA
 
Source name colorectal cancer cells
Organism Homo sapiens
Characteristics cell line: COLO-320
chip antibody: none
Growth protocol COLO-320 cells were maintained at 37C in media of RPMI-1640 supplemented with 10% fetal bovine serum.
Extracted molecule genomic DNA
Extraction protocol For chromatin immunoprecipitation, approximately 5 x 10^7 cells were fixed in 1% formaldehyde, and chromatin was sheared by sonication for 15 alternating on-off cycles of 30 seconds using a Bioruptor (Diagenode). Sheared chromatin from approximately 1 x 10^6 cells was used for each ChIP assay. ChIP was performed using two independent antibodies against human CDX2: a rabbit polyclonal antibody (Cell Signaling) and a mouse monoclonal antibody (Biogenex CDX2-88). ChIP and input DNA were prepared into libraries and sequenced using a Genome Analyzer IIx (Illumina), according to manufacturer protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description input DNA
Data processing Alignment: Sequence reads were obtained and mapped to the unmasked human genome (hg18) using the Illumina Genome Analyzer Pipeline (ELAND Extended).
Peaks: Peak detection was performed with the QuEST algorithm (Valouev et al. Nat Methods 2008)
 
Submission date Jun 16, 2011
Last update date May 15, 2019
Contact name Keyan Salari
E-mail(s) ksalari@mgh.harvard.edu
Organization name Massachusetts General Hospital
Street address Gray/Bigelow Rm 1102, 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL10999
Series (2)
GSE30026 CDX2 ChIP-seq
GSE30475 Colorectal Cancer Cells
Relations
SRA SRX077858
BioSample SAMN00627829

Supplementary file Size Download File type/resource
GSM743038_100816_HWUSI-EAS270R_0019_629BBAAXX_L2_eland_extended_pf.txt.gz 456.2 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