Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARRB1

Cell type

Cell type Class
Prostate
Cell type
C4-2
Tissue
Prostate
Cell Type
Epithelial
Disease
Prostate Cancer

Attributes by original data submitter

Sample

source_name
C4-2_ARRB1 ChIP
cell line
C4-2
cell type
immortalised prostate epithelial cells
genotype/variation
parental, endogenous levels of ARRB1
factor
ARRB1
cuture condition
untreated, cultured in RPMI+10%FBS
chip antibody
A1CT anti-ARRB1 gift from Pr R. Lefkowitz

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. 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 15 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 Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
26810853
Reads aligned (%)
94.0
Duplicates removed (%)
3.1
Number of peaks
1192 (qval < 1E-05)

hg38

Number of total reads
26810853
Reads aligned (%)
95.7
Duplicates removed (%)
2.0
Number of peaks
987 (qval < 1E-05)

Base call quality data from DBCLS SRA