Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ONECUT2

Cell type

Cell type Class
Prostate
Cell type
22Rv1
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
22Rv1 - prostate carcinoma
cell line
22Rv1
chip antibody
Anti-ONECUT2 antibody produced in rabbit (Sigma-Aldrich, catalog#)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
104230520
Reads aligned (%)
84.1
Duplicates removed (%)
10.8
Number of peaks
3066 (qval < 1E-05)

hg38

Number of total reads
104230520
Reads aligned (%)
85.5
Duplicates removed (%)
9.9
Number of peaks
4527 (qval < 1E-05)

Base call quality data from DBCLS SRA