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Sample GSM2571990 Query DataSets for GSM2571990
Status Public on Oct 26, 2018
Title 22RV1-OC2-1
Sample type SRA
Source name 22Rv1 - prostate carcinoma
Organism Homo sapiens
Characteristics cell line: 22Rv1
chip antibody: Anti-ONECUT2 antibody produced in rabbit (Sigma-Aldrich, catalog#)
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 Chromatin IP against ONECUT2
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
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
BioSample SAMN06702996
SRA SRX2731586

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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