|
| Status |
Public on Jun 09, 2015 |
| Title |
MDA-MB-453_H3K27me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-453
cell type: Luminal cells
chip-antibody: H3K27me3
chip-antibody vendor: CST
chip-antibody cat. #: C36B11
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and the DNA was fragmented with a Covaris S2 (Covaris). The fragmented DNA was incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by AMPureXP Agencourt Bioscience). ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and adaptor oligo (Life technologies) was ligated and subjected to PCR amplification (15 cycles) using specific primers provided by the Life technologies. The PCR product was purified with AMPureXP and the emulsion PCR performed according to the manufacturer's instructions and sequenced by SOLiD4 (Life technologies).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
Basecalls performed using the SOLiD4 Pipeline.
ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using bowtie version 0.12.7 with default configuration.
peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default).
Genome_build: hg18
Supplementary_files_format_and_content: Bed files were generated using SICER. Each raw represents each peak detected by SICER. Numbers in the fifth column represent enrichment scores calculated by SICER.
|
| |
|
| Submission date |
Apr 08, 2015 |
| 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 |
GPL13393 |
| Series (2) |
| GSE38548 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer |
| GSE38789 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 2] |
|
| Relations |
| BioSample |
SAMN03466596 |
| SRA |
SRX984108 |
