SRX2370660
GSM2400357: DNase-seq from RKO (ENCLB307RIV); Homo sapiens; DNase-Hypersensitivity

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
DNase-seq
Antigen
DNase-Seq

Cell type

Cell type Class
Digestive tract
Cell type
RKO
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

dev stage
unknown
cell line
RKO
sex
not collected
sample type
immortalized cell line
donor ID
ENCDO035MMY
age
unknown
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
256947791
Reads aligned (%)
59.6
Duplicates removed (%)
37.8
Number of peaks
96731 (qval < 1E-05)

hg19

Number of total reads
256947791
Reads aligned (%)
59.2
Duplicates removed (%)
38.4
Number of peaks
95790 (qval < 1E-05)

Base call quality data from DBCLS SRA