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| 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
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| 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.
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| 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.
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| Contributor(s) |
Chi P, Chen Y, Zheng D, Allis CD, Sawyers CL |
| Citation(s) |
20927104 |
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| Submission date |
Jun 18, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
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| Phone |
646-888-3356
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Human Oncology and Pathogenesis Program
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| Lab |
Chen
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| Street address |
1275 York Ave, Box 20
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE22852 |
Gastrointestinal stromal tumor GIST: gene expresssion and ChIP analyses |
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| Relations |
| SRA |
SRP002829 |
| BioProject |
PRJNA129281 |
