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Sample GSM2127441 Query DataSets for GSM2127441
Status Public on Apr 15, 2018
Title GIST-T1 ETV1 IP
Sample type SRA
 
Source name GIST-T1 Human GIST Cells
Organism Homo sapiens
Characteristics cell line: GIST-T1
antibody: ETV1
Treatment protocol Cells were harvested in log phase growth
Growth protocol Cells were grown in 10% FBS
Extracted molecule genomic DNA
Extraction protocol Chromatin was isolated and sheared. For ETV1 IP, chromatin was IP'd using anti-ETV1 antibody (abcam ab81086) and magnetic protein A/G beads.The immunoprecipate was washed and eluted using standing conditions.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing The sequenced reads from fastq files were mapped to hg19 using Bowtie 1.0
Peaks were called using MACS2. Downstream analysis were performed using Homer and SeqMiner
Genome_build: Hg19
Supplementary_files_format_and_content: ENCODE narrowPeak: Narrow (or Point-Source) Peaks format. See https://genome.ucsc.edu/FAQ/FAQformat.html
 
Submission date Apr 19, 2016
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
 
Platform ID GPL11154
Series (1)
GSE80443 ETV1 binding sites in GIST and Melanoma cells
Relations
BioSample SAMN04886704
SRA SRX1721484

Supplementary file Size Download File type/resource
GSM2127441_T1_ETV1_MACS_peaks.narrowPeak.gz 354.8 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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