Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Enterocytes
MeSH Description
Absorptive cells in the lining of the INTESTINAL MUCOSA. They are differentiated EPITHELIAL CELLS with apical MICROVILLI facing the intestinal lumen. Enterocytes are more abundant in the SMALL INTESTINE than in the LARGE INTESTINE. Their microvilli greatly increase the luminal surface area of the cell by 14- to 40 fold.

Attributes by original data submitter

Sample

source_name
enterocyte from adult mice
strain
mixed C57BL/6 CD1
tissue
small intestine
age
P60
cell type
enterocyte
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[Samples E14.5 and E12.5] Single cell suspensions of embryonic cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K27Ac (Abcam 4729) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform. [Samples AE and ISC] Single cell suspensions of adult cells were fixed for 10 min with 1% PFA at RT, washed twice with PBS and stained with PerCP-eFluor® 710–conjugated anti-EpCAM 1:400 (eBioscience), PE-conjugated anti-CD45 at 1:400 (BD Biosciences) and anti-CD31 at 1:400 (BD Biosciences) antibody for 15-30 min at RT. Two hundred fifty thousand EpCAM+ embryonic intestinal cells, Lgr5-EGFPhigh ISCs or enterocytes were isolated by FACS and stored at -80°C. To obtain fragments around 350-700 bp, chromatin was resuspended in 150 uL of sonication buffer (1% SDS, 50 mM Tris-Cl pH 8.0, 10 mM EDTA) and sonicated for 56 cycles 10 sec ON/ 90 sec OFF (Diagenode) at 4C. H3K27Ac (Abcam 4729) antibodies were used. 20 uL of Protein A/G sepharose beads (Sigma, P6486 and E3403) were pre-incubated for 3 hours with 0.5 ug of antibody in RIPA buffer, then washed3 times with RIPA buffer. The sonicated chromatin was diluted till final volume 750 uL and incubated with antibody-bead slurry at 4C overnight. Beads were washed 3 times with 1 mL of RIPA buffer and once with TE. DNA was eludet and incubated with RNAse A for 30 min, followed by ON incubation with PK. DNA was extracted using phenol: chloroform. Libraries were prepared using NuGEN Ovation Ultralow Library System V2 (NuGEN) according to manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
52658898
Reads aligned (%)
98.7
Duplicates removed (%)
18.1
Number of peaks
522 (qval < 1E-05)

mm9

Number of total reads
52658898
Reads aligned (%)
98.4
Duplicates removed (%)
18.0
Number of peaks
628 (qval < 1E-05)

Base call quality data from DBCLS SRA