Antigen

Antigen Class

Histone

Antigen

H3

Cell type

Cell type Class

Digestive tract

Cell type

Duodenum

MeSH Description

The shortest and widest portion of the SMALL INTESTINE adjacent to the PYLORUS of the STOMACH. It is named for having the length equal to about the width of 12 fingers.

Sample

source_name

Small intestine; duodenum

tissue

duodenum

primary cell type

enterocyte

chip-antibody

H3

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Mini-gut organoids were isolated from Matrigel with Cell Recovery Solution (Corning 354253). Cells were cross-linked with formaldehyde and nuclei were isolated, lysed, and sonicated with a Covaris S220 ultrasonicator. The resulting nuclear extract was incubated overnight at 4 C with Dynal Protein G beads pre-incubated with 5µg of anti-H3 antibody. Beads were washed and bound complexes eluted, and cross-links were reversed by heating to 65 C. IP and input DNA were then purified by a treatment with RNAse A, proteinase K, and phenol:chloroform extraction. Libraries were constructed from IP and input DNA by NEBnext® Ultra™ DNA-library preparation kit for Illumina and subjected to 50 bp single-end read sequencing with Illumina Hiseq 2000.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

43192228

Reads aligned (%)

98.2

Duplicates removed (%)

21.1

Number of peaks

520 (qval < 1E-05)

mm9

Number of total reads

43192228

Reads aligned (%)

97.8

Duplicates removed (%)

20.9

Number of peaks

599 (qval < 1E-05)