Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Prostate
Cell type
PC-3
Primary Tissue
Prostate
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

dev stage
adult
cell line
PC-3
sex
male
sample type
immortalized cell line
donor ID
ENCDO349AAA
age
62 year
health state
grade IV, adenocarcinoma
lab
John Stamatoyannopoulos, UW

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
other: https://www.encodeproject.org/documents/926174f5-d14c-4e77-bc52-5517b56daac0/@@download/attachment/Culturedcells_SOP_nuclei_DNase_crosslink_RNA_V1.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
406960348
Reads aligned (%)
85.2
Duplicates removed (%)
61.5
Number of peaks
194250 (qval < 1E-05)

hg19

Number of total reads
406960348
Reads aligned (%)
84.8
Duplicates removed (%)
62.5
Number of peaks
191813 (qval < 1E-05)

Base call quality data from DBCLS SRA