Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

Cell type

Cell type Class
Digestive tract
Cell type
Intestinal crypt
NA
NA

Attributes by original data submitter

Sample

source_name
small intestine
genotype/variation
wild type
antibody
H3K9me3 - ab8898 Abcam
strain
C57BL/6
cell type
whole crypt isolate

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sonication was performed in 180 μl of lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA,1% SDS and protein inhibitors cocktail) in a water-cooled Bioruptor (Diagenode), high power, with 14 cycles with 30 seconds on and 30 seconds off each. The sonicated chromatin was diluted in 810 ul of RIPA buffer containing 0.1% SDS and incubated overnight with protein A/G sepharose Dynabeads previously incubated with the specific antibody for ChIP (H3K9me2 - ab1220 and H3K9me3 - ab8898 Abcam) for 2 hours. For the inputs 3% of the volume for each sample was used. Following incubation, the material was washed 2 times with RIPA buffer low salt (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton-X-100, 0.1 % SDS ) and 2 times with RIPA buffer high salt (containing 500 mM NaCl) and once with TE buffer (10 mM Tris-HCl, 1 mM EDTA). Samples were diluted in 200 μl of elution buffer (20 mM Tris-HCl pH 7.5, 5 mM EDTA and 50 mM NaCl) and treated with 2 μl of RNase (20 mg/ml) for 30 minutes at 37 °C. After, samples was incubated with protein k for 2 hours at 65 °C at 300 rpm. The DNA was extracted with phenol-chloroform protocol. Libraries were generated from 5 ng total chromatin according to NEBNext UltraII DNA Library Prep kit for Illumina. Libraries were sequenced on an Illumina HiSeq as 100 bp Paired End reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
64545531
Reads aligned (%)
96.4
Duplicates removed (%)
42.5
Number of peaks
1100 (qval < 1E-05)

mm9

Number of total reads
64545531
Reads aligned (%)
96.2
Duplicates removed (%)
43.2
Number of peaks
1072 (qval < 1E-05)

Base call quality data from DBCLS SRA