Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HAND1

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
chip antibody
HAND1, Origene, OTI1G10

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon) for ChIP-seq or Nextera DNA Preparation Kit (Illumina) for ATAC-seq.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
35464364
Reads aligned (%)
90.6
Duplicates removed (%)
5.7
Number of peaks
9059 (qval < 1E-05)

hg38

Number of total reads
35464364
Reads aligned (%)
92.3
Duplicates removed (%)
4.5
Number of peaks
9273 (qval < 1E-05)

Base call quality data from DBCLS SRA