Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

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

Attributes by original data submitter

Sample

source_name
Prostate cancer cell line LNCaP
cell line
LNCaP
passage
14-17
digestion level
25U
fragment size
100-200bp

Sequenced DNA Library

library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase
library_construction_protocol
LNCaP and MCF-7 cells were harvested by trypsinization followed by nuclei extraction. Entact nuclei were treated with Dnase I for desired time. Libraries were prepared according to Rubicon's instructions accompanying the ThruPLEX-FD kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
50042876
Reads aligned (%)
94.1
Duplicates removed (%)
54.7
Number of peaks
13955 (qval < 1E-05)

hg19

Number of total reads
50042876
Reads aligned (%)
93.2
Duplicates removed (%)
56.0
Number of peaks
13593 (qval < 1E-05)

Base call quality data from DBCLS SRA