Antigen

Antigen Class

DNase-seq

Antigen

DNase-Seq

Cell type

Cell type Class

Pancreas

Cell type

Islets of Langerhans

MeSH Description

Irregular microscopic structures consisting of cords of endocrine cells that are scattered throughout the PANCREAS among the exocrine acini. Each islet is surrounded by connective tissue fibers and penetrated by a network of capillaries. There are four major cell types. The most abundant beta cells (50-80%) secrete INSULIN. Alpha cells (5-20%) secrete GLUCAGON. PP cells (10-35%) secrete PANCREATIC POLYPEPTIDE. Delta cells (~5%) secrete SOMATOSTATIN.

Sample

source_name

Pancreatic islet

strain

C57BL/6

tissue

Pancreatic islet

Sequenced DNA Library

library_strategy

DNase-Hypersensitivity

library_source

GENOMIC

library_selection

DNase

library_construction_protocol

ChIP was performed according to the “Mammalian ChIP-on-chip” protocol (Agilent) using a polyclonal antibody against Nrf1 antibody (ab34682, Abcam) and Protein G Dynabeads (Life Technologies). 10-100 million cells were used for each experiment. qPCR using positive and negative control primers was performed to ensure ChIP enrichment. Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter. DNase-seq was performed as described previously (Sherwood et al., 2014 PMID 24441470). 10-100 million cells were digested with 60-100 units of DNase I (Promega) per 107 nuclei. 50-125 bp hypersensitive DNA was collected using E-Gel SizeSelect Agarose 2% gels (Life Technologies). Library preparation and Illumina HiSeq were performed by the MIT BioMicroCenter.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

190956678

Reads aligned (%)

1.8

Duplicates removed (%)

15.6

Number of peaks

5185 (qval < 1E-05)

mm9

Number of total reads

190956678

Reads aligned (%)

1.8

Duplicates removed (%)

16.0

Number of peaks

5187 (qval < 1E-05)