Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Prostate
Cell type
PrEC
Tissue
prostate
Lineage
epithelial
Description
prostate epithelial cell line

Attributes by original data submitter

Sample

source_name
PrEC
cell line
PrEC
chip antibody
H3K4me3 (#39160, Active Motif)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were purified (described for NOMe-Seq) after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP. Libraries for ChIP-Seq were prepared by the USC Epigenome Center following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
55741699
Reads aligned (%)
84.6
Duplicates removed (%)
21.9
Number of peaks
30487 (qval < 1E-05)

hg19

Number of total reads
55741699
Reads aligned (%)
82.5
Duplicates removed (%)
25.1
Number of peaks
29799 (qval < 1E-05)

Base call quality data from DBCLS SRA