Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Small intestine
NA
NA

Attributes by original data submitter

Sample

source_name
EpCAM+ epithelium from small intestine
strain
mixed C57BL/6 CD1
tissue
small intestine
age
E14.5
cell type
intestinal epithelial cell
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. H3K4me3 (Millipore #07-473) 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. H3K4me3 (Millipore #07-473) 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
60646807
Reads aligned (%)
95.2
Duplicates removed (%)
16.4
Number of peaks
660 (qval < 1E-05)

mm9

Number of total reads
60646807
Reads aligned (%)
95.0
Duplicates removed (%)
16.3
Number of peaks
734 (qval < 1E-05)

Base call quality data from DBCLS SRA