SRX2370814
GSM2400512: DNase-seq from SK-N-DZ (ENCLB534QSX); 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
NextSeq 500

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
306362484
Reads aligned (%)
2.5
Duplicates removed (%)
17.8
Number of peaks
10570 (qval < 1E-05)

hg19

Number of total reads
306362484
Reads aligned (%)
2.5
Duplicates removed (%)
18.6
Number of peaks
10517 (qval < 1E-05)

Base call quality data from DBCLS SRA