SRX2370603
GSM2400286: DNase-seq from HepG2 (ENCLB029COU); Homo sapiens; DNase-Hypersensitivity

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

dev stage
child
cell line
HepG2
sex
male
sample type
immortalized cell line
donor ID
ENCDO000AAC
age
15 year
health state
hepatocellular carcinoma
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 2000

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
366011413
Reads aligned (%)
73.4
Duplicates removed (%)
43.5
Number of peaks
114017 (qval < 1E-05)

hg19

Number of total reads
366011413
Reads aligned (%)
73.0
Duplicates removed (%)
44.1
Number of peaks
112928 (qval < 1E-05)

Base call quality data from DBCLS SRA