Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Jejunum
MeSH Description
The middle portion of the SMALL INTESTINE, between DUODENUM and ILEUM. It represents about 2/5 of the remaining portion of the small intestine below duodenum.

Attributes by original data submitter

Sample

source_name
Jejunum
genotype/variation
WT
cell type
intestinal epithelial cells
chip antibodies
none
mice strain
C57BL/6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
IECs were isolated with a modified method (Goodyear AW, et al. J Immunol Methods 2014;405:97-108). Dissociated IECs were collected by centrifugation. IECs were freshly isolated from both DIECUN and F/FUN neonates at P12 and were subjected to ChIP (MAGnify ChIP system, ThermoFisher). After reverse cross-linking, library preparation was carried out by using the MicroPlex Library Preparation Kit V2 (Diagenode, C05010012). Cluster generation and 50 cycles of single end sequencing were carried out on an Illumina Nexseq 500. Sequence tags were aligned (mapped) to the unmasked mouse (mm9) or human (hg19) reference genome.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
103177225
Reads aligned (%)
97.3
Duplicates removed (%)
16.8
Number of peaks
519 (qval < 1E-05)

mm9

Number of total reads
103177225
Reads aligned (%)
97.1
Duplicates removed (%)
16.7
Number of peaks
688 (qval < 1E-05)

Base call quality data from DBCLS SRA