|
| Status |
Public on Jun 17, 2014 |
| Title |
MCF7_JARID1BChIP_siJARID1B |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
chip antibody: JARID1B (Novus Biologicals, 22260002)
transfection: siJARID1B
|
| Treatment protocol |
Cells transfected with gene-specific or non-targeting siRNA pools were cultured for 5 days prior to the sample preparation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Covaris focused-ultrasonicator. Following ChIP performed with specific antibodies and Dynabeads® Protein G (Invitrogen)
ChIP DNA was subjected to end repair, A-tailing, ligation of Illumia single end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7 or 1.8.
ChIP-seq raw data was mapped by Bowtie using default parameters to hg19.
Each library after mapping was randomly sampled down without replacement to 15 million reads. Only one tag from each unique position was considered to avoid PCR biases from the sequencing.
The identification of ChIP-seq enriched regions including summits was performed using version 2.0 of MACS. Regions of enrichment comparing to input control exceeding a given threshold (q < 0.001) were called as peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files of called peaks were generated using MACS2
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE46055 |
Genome-wide location analysis in breast cancer cell-lines |
| GSE46073 |
Gene expression and genome-wide location analysis of breast cancer cell-lines |
|
| Relations |
| BioSample |
SAMN02045873 |
| SRA |
SRX265413 |
