ChIP-Atlas: SRX100893

Sample information curated by ChIP-Atlas

Antigen

Antigen Class: DNase-seq
Antigen: DNase-Seq

Cell type

Cell type Class: Epidermis
Cell type: NHEK
Tissue: skin
Lineage: ectoderm
Description: epidermal keratinocytes

Attributes by original data submitter

Sample

source_name: NHEK
biomaterial_provider: Lonza
datatype: DnaseSeq
datatype description: DNaseI HS Sequencing
controlid: generic_female
labversion: baseAlignCounts.pl v 1,1% ENCODE array platform validation tests,p-value cutoff: 0.05,fseq v 1.84, iff_generic_female
replicate: 1,2
cell organism: human
cell description: epidermal keratinocytes
cell karyotype: normal
cell lineage: ectoderm
cell sex: U
treatment: None
treatment description: No special treatment or protocol applies
controlid: generic_female
labversion: align_on_cluster_bwa.pl v 1
replicate: 1
replicate description: tier 1

Sequenced DNA Library

library_name: GSM816635: Duke_DnaseSeq_NHEK
library_strategy: DNase-Hypersensitivity
library_source: GENOMIC
library_selection: DNase

Sequencing Platform

instrument_model: Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads: 53555638
Reads aligned (%): 98.3
Duplicates removed (%): 6.9
Number of peaks: 0 (qval < 1E-05)

hg19

Number of total reads: 53555638
Reads aligned (%): 98.2
Duplicates removed (%): 7.4
Number of peaks: 9334 (qval < 1E-05)

Base call quality data from DBCLS SRA