Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pancreas
Cell type
Pancreatic islets
NA
NA

Attributes by original data submitter

Sample

source_name
Human islets
tissue
pancreatic islets
diagnosis
Healthy

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Islets were washed twice with ice cold 1xPBS by spinning at 500g for 5mins at 4°C. Cell lysis was performed with ATAC lysis buffer (10mM Tris-HCl, pH 7.4, 3mM MgCl2, 10mM NaCl and 0.1% IGEPAL CA-630) by incubating on ice for 10mins and nuclei were then collected by spinning at 500g for 10mins at 4°C. The transposition reaction mix (12.5μl of 2X TD buffer, 2μl of Tn5 transposase (Illumina, San Diego, CA, USA) and 10.5μl of nuclease free water was added to nuclei and incubated at 37°C for 1hour before the reaction was cleaned using MinElute cleanup kit (Qiagen, Hilden, Germany). Next, 10-12cycles of PCR were performed with transposed DNA using the Illumina Nextera dual index primers. The PCR product was cleaned using PCR purification kit (Qiagen).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
170941945
Reads aligned (%)
35.2
Duplicates removed (%)
12.3
Number of peaks
5800 (qval < 1E-05)

hg19

Number of total reads
170941945
Reads aligned (%)
34.8
Duplicates removed (%)
12.6
Number of peaks
4653 (qval < 1E-05)

Base call quality data from DBCLS SRA