Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Liver
Cell type
HuH-7
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

source_name
Huh-7
biomaterial_provider
Dr. Ravi Jhaveri at Duke University
datatype
DnaseSeq
datatype description
DNaseI HS Sequencing
cell description
hepatocellular carcinoma
controlid
generic_male
labversion
baseAlignCounts.pl v 1,fseq v 1.84, iff_generic_male,p-value cutoff: 0.05
replicate
1,2
cell description
Hepatocellular carcinoma
cell karyotype
cancer
cell lineage
endoderm
cell sex
M
controlid
generic_male
labversion
align_on_cluster_bwa.pl v 1
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM816641: Duke_DnaseSeq_Huh-7
library_strategy
DNase-Hypersensitivity
library_source
GENOMIC
library_selection
DNase

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
138098656
Reads aligned (%)
0.9
Duplicates removed (%)
20.4
Number of peaks
408 (qval < 1E-05)

hg19

Number of total reads
138098656
Reads aligned (%)
0.8
Duplicates removed (%)
20.5
Number of peaks
418 (qval < 1E-05)

Base call quality data from DBCLS SRA