SRX2156862
GSM2308450: DNase-seq from Karpas-422 (ENCLB613MEH); Homo sapiens; DNase-Hypersensitivity

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Blood
Cell type
KARPAS-422
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma Non-Hodgkins

Attributes by original data submitter

Sample

age
73 year
dev stage
adult
donor ID
ENCDO354AAA
sex
female
health state
human B cell non-Hodgkin's lymphoma
sample type
immortalized cell line
cell line
Karpas-422
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
375992022
Reads aligned (%)
78.2
Duplicates removed (%)
66.9
Number of peaks
84153 (qval < 1E-05)

hg19

Number of total reads
375992022
Reads aligned (%)
77.5
Duplicates removed (%)
68.6
Number of peaks
83869 (qval < 1E-05)

Base call quality data from DBCLS SRA