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Sample GSM558678 Query DataSets for GSM558678
Status Public on Oct 14, 2010
Title ETV1-ChIPSeq
Sample type SRA
 
Source name GIST48 Cells, ChIP fraction
Organism Homo sapiens
Characteristics cell line: GIST
fraction: ChIP fraction
chip antibody: anti-ETV1 (Abcam Ab81086, lot#787879)
Growth protocol GIST48 cells were continued passaged. 1E8 cells were used.
Extracted molecule genomic DNA
Extraction protocol Crosslinking ChIP was performed as described (Lee et al. 2006). Briefly, GIST cells were harvested and crosslinked in 1% paraformaldehyde for 15 minutes, pellets flash-frozen in liquid nitrogen, and stored at -80 degrees C. Chromatin was isolated and sheared to 200-700 bp using a Bioruptor (Diagenode), and ChIP was performed as described (Lee et al. 2006). Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with anti-ETV1 antibody (Abcam Ab81086, Lot 787879), washed, eluted, reverse cross-linked, and purified. Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR. Following isolation of ChIP DNA, libraries were prepared for cluster generation as described (Goldberg et al. 2010). Purified DNA libraries were used for cluster generation on Illumina/Solexa flow cells, and sequencing analysis was performed on an Illumina/Solexa Genome Analyzer 2 following manufacturer protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against ETV1
Data processing All reads (~36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline. Unique reads mapped to a single best-matching location with no more than two mismatches were kept and used to generate genome-wide distribution of ETV1-binding and for peak identification. Redundant reads were considered once.
 
Submission date Jun 22, 2010
Last update date May 15, 2019
Contact name Yu Chen
E-mail(s) cheny1@mskcc.org
Phone 646-888-3356
Organization name Memorial Sloan Kettering Cancer Center
Department Human Oncology and Pathogenesis Program
Lab Chen
Street address 1275 York Ave, Box 20
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL9115
Series (2)
GSE22441 Mapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).
GSE22852 Gastrointestinal stromal tumor GIST: gene expresssion and ChIP analyses
Relations
SRA SRX023216
BioSample SAMN00016959

Supplementary file Size Download File type/resource
GSM558678_GIST48_ETV1_ChIP.bed.gz 196.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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