|
| Status |
Public on Sep 05, 2014 |
| Title |
KATOIII Input |
| Sample type |
SRA |
| |
|
| Source name |
KATOIII Input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KATOIII
cell type: gastric cancer
chip antibody: none
|
| 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 |
SAMN02384053 |
| SRA |
SRX367643 |
