|
| 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 02.14.01.07 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
Genome_build:hg19
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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN03159557 |
| SRA |
SRX878129 |
