SRX2370815
GSM2400513: DNase-seq from SK-N-DZ (ENCLB799DVF); Homo sapiens; DNase-Hypersensitivity

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Neural
Cell type
SK-N-DZ
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

dev stage
child
cell line
SK-N-DZ
sex
female
sample type
immortalized cell line
donor ID
ENCDO340AAA
age
2 year
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

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
243593983
Reads aligned (%)
3.5
Duplicates removed (%)
17.0
Number of peaks
15056 (qval < 1E-05)

hg19

Number of total reads
243593983
Reads aligned (%)
3.5
Duplicates removed (%)
17.7
Number of peaks
15043 (qval < 1E-05)

Base call quality data from DBCLS SRA