Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
Pancreatic islets
NA
NA

Attributes by original data submitter

Sample

source_name
FACS-sorted pancreatic islet
tissue
pancreatic islets
cell type
Beta
donor id
CITH070
chip-seq antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
We performed FACS sorting on dispersed human islets using cell surface antibodies (1:20) and secondary antibodies (1:200; 115-116-075, 115-135-164, Jackson ImmunoResearch) as described before (Dorrell C, et al. Stem Cell Res 2008) to obtain cell populations highly enriched for alpha, beta, and exocrine (duct and acinar) cells. Total RNA was isolated from whole islets, and sorted alpha, beta, and exocrine cells using the Ambion mirVana miRNA Isolation Kit (AM1560) reverse transcribed to cDNA using SuperScript II reverse transcriptase (Invitrogen). ChIP and preparation of ChIP-Seq libraries was performed on individual cell sorts for each cell type and donor (H3K4me3: 8580, Abcam; H3K27me3: 07-449. Upstate). DNA from ChIP or reverse transcription was treated by blunt end repair and ligation of sequencing adapters. Adapter-ligated fragments were size select to roughly 200bp and amplified by PCR. Final libraries were verified on an Agilent Technologies 2100 BioAnalyzer to check size, purity, and concentration of the library prior to sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
24564221
Reads aligned (%)
81.7
Duplicates removed (%)
41.8
Number of peaks
583 (qval < 1E-05)

hg19

Number of total reads
24564221
Reads aligned (%)
80.8
Duplicates removed (%)
43.3
Number of peaks
836 (qval < 1E-05)

Base call quality data from DBCLS SRA