Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARRB1

Cell type

Cell type Class
Prostate
Cell type
Prostate
MeSH Description
A gland in males that surrounds the neck of the URINARY BLADDER and the URETHRA. It secretes a substance that liquefies coagulated semen. It is situated in the pelvic cavity behind the lower part of the PUBIC SYMPHYSIS, above the deep layer of the triangular ligament, and rests upon the RECTUM.

Attributes by original data submitter

Sample

source_name
prostate tissue_ARRB1 ChIP
tissue
human prostate tissue
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
26659574
Reads aligned (%)
89.4
Duplicates removed (%)
7.1
Number of peaks
1148 (qval < 1E-05)

hg38

Number of total reads
26659574
Reads aligned (%)
91.0
Duplicates removed (%)
6.1
Number of peaks
901 (qval < 1E-05)

Base call quality data from DBCLS SRA