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 cancer cell line
tissue
prostate cancer cell line
cell line
LNCaP
treatment
UPF-1069
chip-antibody
FOXA1 (Abcam, ab23738)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Protein-DNA complexes were isolated from sonicated LNCaP cell lysates with indicated antibodies, and the ChIP DNA was extracted using phenol chloroform extraction method. Purified ChIP DNA was dissolved in TE buffer and re-sheared using Covaris sonicator to enable enrichment of fragments with an average size of 300 bp. The re-sheared DNA samples were purified for library preparation using the minElute PCR purification kit (Qiagen). The ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics; R400427) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
39346503
Reads aligned (%)
88.0
Duplicates removed (%)
4.4
Number of peaks
13854 (qval < 1E-05)

hg38

Number of total reads
39346503
Reads aligned (%)
90.2
Duplicates removed (%)
3.0
Number of peaks
13893 (qval < 1E-05)

Base call quality data from DBCLS SRA