Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Prostate
Cell type
PC-3
Primary Tissue
Prostate
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
PC3
cell line
PC3
chip antibody
CTCF (#07-729, Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were purified (described for NOMe-Seq) after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP. Libraries for ChIP-Seq were prepared by the USC Epigenome Center following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
34620441
Reads aligned (%)
71.3
Duplicates removed (%)
22.5
Number of peaks
44033 (qval < 1E-05)

hg38

Number of total reads
34620441
Reads aligned (%)
72.8
Duplicates removed (%)
21.4
Number of peaks
44176 (qval < 1E-05)

Base call quality data from DBCLS SRA