Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
HPDE6
Primary Tissue
Pancreas
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
71_Input
clone
71
tissue
pancreatic duct
cell type
pancreatic epithelial cells (HPDE)
source
derived from single cell clone
genotype
ARID1A Wildtype
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with fresh 1% formaldehyde for 10 min at room temperature and 125 mM glycine was added to inactivate the fixation. Cells were washed by cold PBS 3 times and collected. Cross-linked chromatin was sonicated into fragments of a size range between 250 and 500 nucleotides (Covaris). H3K27Ac antibody (Abcam, ab4729) was incubated with the solubilized DNA fragments at 4°C overnight. Antibody–chromatin complexes were captured by protein A/G Agarose beads (Pierce #20423) and eluted with 1% SDS after extensive washing. The cross-link between DNA and chromatin proteins was reversed by incubation overnight at 65°C. DNA was purified by QIAquick PCR Purification Kit (Qiagen 28104) and dissolved into 30 μL TE buffer per immunoprecipitation. ChIP-seq libraries were generated using KAPA LTP library preparation kit(KK8230) following the manufacturer's protocol (Kapa Biosystems).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
32389241
Reads aligned (%)
98.0
Duplicates removed (%)
3.5
Number of peaks
1159 (qval < 1E-05)

hg19

Number of total reads
32389241
Reads aligned (%)
97.0
Duplicates removed (%)
4.9
Number of peaks
1055 (qval < 1E-05)

Base call quality data from DBCLS SRA