Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
prostate cell line
cell line
androgen-dependent prostate cancer derived cell line LNCaP
passage number
32-34
chip antibody
FoxA1 [Abcam 23738]
genotype/variation
control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and AR-DNA or FoxA1-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment 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, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
100568612
Reads aligned (%)
98.8
Duplicates removed (%)
81.5
Number of peaks
53297 (qval < 1E-05)

hg19

Number of total reads
100568612
Reads aligned (%)
98.2
Duplicates removed (%)
82.6
Number of peaks
52759 (qval < 1E-05)

Base call quality data from DBCLS SRA