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Series GSE22441 Query DataSets for GSE22441
Status Public on Oct 14, 2010
Title Mapping of ETV1 genomic binding sites in gastrointestinal stromal tumor (GIST).
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ETV1 is highly expressed in GIST and their presumed precursors--the interstitial cells of Cajal. ETV1 is required for survival for both GIST and ICC and regulates GIST signature genes. Here, using Illumina-Solexa based next-generation sequencing of ETV1 chromatin immunoprecipates (ChIP-Seq), we define ETV1 binding sites in the GIST48 cell line.
 
Overall design Crosslinked ChIP using input control ETV1 ChIP in GIST48 cells.
Details: GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. 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, and sequenced on Solexa Genome Analyzer. 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.
 
Contributor(s) Chi P, Chen Y, Zheng D, Allis CD, Sawyers CL
Citation(s) 20927104
Submission date Jun 18, 2010
Last update date May 15, 2019
Contact name Yu Chen
E-mail(s) cheny1@mskcc.org
Phone 646-888-2163
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
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (2)
GSM558677 input DNA
GSM558678 ETV1-ChIPSeq
This SubSeries is part of SuperSeries:
GSE22852 Gastrointestinal stromal tumor GIST: gene expresssion and ChIP analyses
Relations
SRA SRP002829
BioProject PRJNA129281

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Supplementary file Size Download File type/resource
GSE22441_RAW.tar 484.9 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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