Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZFX

Cell type

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

Attributes by original data submitter

Sample

source_name
22Rv1 cells
cell line
prostate carcinoma epithelial cell line 22Rv1
chip antibody
anti-ZFX serum (from Dr Huck-Hui Ng)
treatment
charcoal stripped

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against AR-FL, AR-V7, BRD4 or ZFX. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for up to 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
77488729
Reads aligned (%)
72.0
Duplicates removed (%)
25.1
Number of peaks
13924 (qval < 1E-05)

hg38

Number of total reads
77488729
Reads aligned (%)
74.4
Duplicates removed (%)
23.2
Number of peaks
14110 (qval < 1E-05)

Base call quality data from DBCLS SRA