Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

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

Attributes by original data submitter

Sample

source_name
LNCaP_H3K4me1 IP
hnf4g status
wildtype
ip
H3K4me1
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

hg38

Number of total reads
51050510
Reads aligned (%)
95.4
Duplicates removed (%)
2.7
Number of peaks
75343 (qval < 1E-05)

hg19

Number of total reads
51050510
Reads aligned (%)
95.1
Duplicates removed (%)
3.0
Number of peaks
77389 (qval < 1E-05)

Base call quality data from DBCLS SRA