Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EZH2

Cell type

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

Attributes by original data submitter

Sample

source_name
LNCaP cells
antibody
EZH2 siRNAs were purchase from Dharmacon as On-target plus siRNA
tissue
LNCaP cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For mouse tissues frozen embedded prostate H&E were assessed for pathology and normal, HGPIN or prostate cancer lesions were core from the frozen blocks and the RNA extracted using RNA simply Kit (Promega). For cell line, RNA extraction was performed using Trizol (Life technology) following manufacturer recommendation. For the ChIp-Seq: Fifty million LNCaP-N-Myc or LNCaP control cells were washed in PBS twice and then fixed using 1% formaldehyde for 8 minutes at room temperature and quenched 5 min using 125 mM glycine. The cells were centrifuged and the cell pellet was resuspended in 2 milliliters of dilution buffer (10mM Tris HCL pH8.0, 0.1% SDS, 1.0mM EDTA with protease and phosphatase inhibitors). Protein-bound chromatin was fragmented by sonication for 15 minutes (Covaris series E220). H3K27me3 antibody was purchase from Diagenode (A1811-001P). Libraries were prepared according to Illumina's instructions

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
59888813
Reads aligned (%)
129.7
Duplicates removed (%)
17.5
Number of peaks
41639 (qval < 1E-05)

hg38

Number of total reads
59888813
Reads aligned (%)
130.7
Duplicates removed (%)
16.8
Number of peaks
41416 (qval < 1E-05)

Base call quality data from DBCLS SRA