Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

dev stage
adult
cell line
SW480
sex
male
sample type
immortalized cell line
donor ID
ENCDO499CXJ
age
50 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

hg38

Number of total reads
199269866
Reads aligned (%)
74.1
Duplicates removed (%)
32.5
Number of peaks
97824 (qval < 1E-05)

hg19

Number of total reads
199269866
Reads aligned (%)
73.6
Duplicates removed (%)
32.8
Number of peaks
97289 (qval < 1E-05)

Base call quality data from DBCLS SRA