|
| Status |
Public on Oct 26, 2018 |
| Title |
22RV1-Input-2 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1 - prostate carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 22Rv1
chip antibody: none
|
| Growth protocol |
22Rv1 were grown in RPMI-1640 media (Gibco) supplemented with 10% FBS and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Concentrated DNA ChIP or Input DNA was ligated to specific annealed linkers followed by direct sequencing using the Illumina HiSeq3000, system at the UCLA Clinical Microarray Core.
ChIP-Seq libraries were prepared with the ChIP-IT High Sensitivity kit from Active Motif. Briefly, 80% confluent 22Rv1 were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to 100-500 bp in a Bioruptor UCD-200 (Diagenode) and incubated overnight with 4μg of antibody (anti-OC2 HPA057058). After RNase A and Proteinase K treatment, ChIP DNA was purified with the column system provided with the kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
input DNA
22RV1-IP-OC2-2.vs.Input_peaks.narrowPeak
|
| Data processing |
Reads were aligned to hg19 with bwa 0.7.13-r1126
Data was filtered with Picard to mark duplicates and filter to q20
permissive peak calls were generated with macs2 2.1.1 and the arguments -p 1e-3 --to-large
the final peak set was generated with IDR 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak files containing permissive peaks of individual replicates + idr peak set
|
| |
|
| Submission date |
Apr 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sungyong You |
| E-mail(s) |
Sungyong.You@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Surgery
|
| Lab |
Freeman Lab.
|
| Street address |
Beverly Blvd 8400
|
| City |
LA |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE97551 |
Genome-wide maps of ONECUT2 binding sites in 22Rv1 human castration resistant prostate cancer cell |
|
| Relations |
| BioSample |
SAMN06702997 |
| SRA |
SRX2731589 |
