Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HNF4G

Cell type

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

Attributes by original data submitter

Sample

source_name
LNCaP_HNF4G IP
hnf4g status
wildtype
ip
HNF4G
cell line
LNCaP

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was isolated and sheared. Following antibodies were used; HNF4G (Sigma; HPA005438 or Proteintech; 25801-1-AP); H3K4me1 (Abcam; ab8895); H3K27ac (Abcam; ab4729); AR (Abcam, ab108341); FOXA1 (Abcam; ab5089). Magnetic protein A/G beadswere used to collect immunoprecipitates. The immunoprecipate was washed and eluted using standing conditions. Purified ChIP DNA was blunt-ended, ligated to adaptors, amplified with 8-12-cycles of PCR, and sequenced.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
68381901
Reads aligned (%)
92.5
Duplicates removed (%)
4.7
Number of peaks
1582 (qval < 1E-05)

hg38

Number of total reads
68381901
Reads aligned (%)
94.9
Duplicates removed (%)
3.0
Number of peaks
1778 (qval < 1E-05)

Base call quality data from DBCLS SRA