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Status |
Public on Oct 14, 2010 |
Title |
ETV1-ChIPSeq |
Sample type |
SRA |
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Source name |
GIST48 Cells, ChIP fraction
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Organism |
Homo sapiens |
Characteristics |
cell line: GIST fraction: ChIP fraction chip antibody: anti-ETV1 (Abcam Ab81086, lot#787879)
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Growth protocol |
GIST48 cells were continued passaged. 1E8 cells were used.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
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Description |
Chromatin IP against ETV1
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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.
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Submission date |
Jun 22, 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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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 |
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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 Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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