NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1250892 Query DataSets for GSM1250892
Status Public on Sep 05, 2014
Title YCC3 GATA4
Sample type SRA
 
Source name YCC3 GATA4
Organism Homo sapiens
Characteristics cell line: YCC3
cell type: gastric cancer
chip antibody: sc-9053
Extracted molecule genomic DNA
Extraction protocol Chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using the antibodies
ChIP-seq libraries were constructed using a ChIP-Seq sample prep kit (IP-102-1001, Illumina) and sequenced on a Genome Analyzer IIx instrument (Illumina)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Illumina Genome Analyzer IIx
Data processing CASAVAv1.8 was used to perform base-calling
ChIP-seq sequence reads were mapped to the human genome using bwa version 0.5.7
Enriched peaks were called using MACS version 1.4.1
Genome_build: hg19
Supplementary_files_format_and_content: bed files included peaks called by MACS for KLF5, GATA4, GATA6 in YCC3, AGS, KATOIII cell lines.
 
Submission date Oct 25, 2013
Last update date May 15, 2019
Contact name Niantao Deng
Organization name Duke NUS Graduate Medical School
Street address Center for Computational Biology, level 6, 8 College Road
City Singapore
State/province Singapore
ZIP/Postal code 169857
Country Singapore
 
Platform ID GPL10999
Series (2)
GSE51705 ChIP-Seq experiments of KLF5, GATA4 and GATA6 in YCC3/AGS/KATOIII cell lines
GSE51706 Integrative study of cooperative lineage-survival oncogenes in gastric cancer
Relations
BioSample SAMN02384050
SRA SRX367637

Supplementary file Size Download File type/resource
GSM1250892_GATA4-YCC3-peaks.bed.gz 206.8 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