Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Prostate
Cell type
DU 145
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
FOXA1_ChIP-seq_DU145 AR C562S+FoxA1
cell line
prostate cancer cell line DU145
ectopic expression
AR C562S +FoxA1
chip antibody
Anti-FOXA1 antibody (Abcam, cat#ab23738,lot# GR77830-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Antibodies were from abcam (cat#ab23738,GR77830-1) and Millipore (cat#06-680, lot#JBC1939961) and ChIP was performed using 5e6-10e6 cells per reaction. Chromatin was fixed in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were washed twice in PBS and scraped before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were sheared to 200-700bp using an ultrasonic sonicator (Misonix). ChIP was done with 5 micrograms of antibody. FAIRE analysis was performed according to the protocol published by Giresi et al . Libraries were prepared according to Bioo Scientific's instructions accompanying the DNA Sample Kit (Part# 514101). 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 (3' to 5' 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 Illumina HiSeq 2000 or Illumina HiSeq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
19483391
Reads aligned (%)
84.5
Duplicates removed (%)
6.5
Number of peaks
73467 (qval < 1E-05)

hg38

Number of total reads
19483391
Reads aligned (%)
85.1
Duplicates removed (%)
6.5
Number of peaks
73657 (qval < 1E-05)

Base call quality data from DBCLS SRA