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Sample GSM1536045 Query DataSets for GSM1536045
Status Public on Nov 09, 2015
Title SOX15 ChIP (ChIP-Seq)
Sample type SRA
Source name CPA cells
Organism Homo sapiens
Characteristics cell line: Barrett's esophagus cell line, CPA
pulldown: Bio-SOX15 was pulled down using Dynabeads MyOne Streptavidin T1 for six hours at 4 degrees (Invitrogen, catalog number 65601)
Extracted molecule genomic DNA
Extraction protocol Cells were harvested and stored at -80°C for subsequent sonication and ChIP. Cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG, Pierce 20593) in PBS for 45 min, followed by 10 min with 1% formaldehyde (Pierce 28906) in PBS, at room temperature. ChIP and ChIP-seq were performed as described previously (Kim et al., 2009), using 30 μL slurry of streptavidin-conjugated magnetic beads (Invitrogen 65601).
Rubicon Truplex-fd preo kit was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description Sample name: Bio SOX15 ChIP
Data processing base-calling: bcl2fastq, version for Illumina NextSeq 500 with default settings.
alignment: Bowtie2, version 2.1.0 with default settings; removed multiply mapped reads and pcr duplicates
peak-calling: macs, version 1.4.1 using -S and -w
Supplementary_files_format_and_content: [ChIP-Seq] bed and wig files
Submission date Oct 31, 2014
Last update date May 15, 2019
Contact name Ramesh Shivdasani
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Shivdasani
Street address 450 Brookline Ave. Dana 720D
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL18573
Series (1)
GSE62909 SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas
BioSample SAMN03159557
SRA SRX878129

Supplementary file Size Download File type/resource
GSM1536045_Bio.Sox15-peaks.bed.gz 73.6 Kb (ftp)(http) BED
GSM1536045_Bio.Sox15.wig.gz 145.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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