Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Digestive tract
Cell type
GIST-T1
NA
NA

Attributes by original data submitter

Sample

source_name
KIT-dependent GIST cell line
cell line
GIST-T1
tissue
Gastrointestinal stromal tumor (GIST) cell line

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Nuclei were incubated with Nextera transposase (Illumina) and DNA prepared per manufacturers recommendations. Libraries for paired-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a Nextera DNA Preparation Kit (Illumina) for ATAC-seq.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
55029644
Reads aligned (%)
65.5
Duplicates removed (%)
43.0
Number of peaks
22976 (qval < 1E-05)

hg19

Number of total reads
55029644
Reads aligned (%)
65.2
Duplicates removed (%)
43.1
Number of peaks
22700 (qval < 1E-05)

Base call quality data from DBCLS SRA