Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me2

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse embryonic stem cells RGd2
cell line
RGd2
cell type
mouse embryonic stem cells
chip antibody
H3K9me2 (Abcam, ab1220)
genotype
WT
time point
32h N2B27

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde and neutralized with glycine to a final concentration of 0.125 mM. After nuclei extraction, DNA for ChIPs of endogenous proteins and corresponding inputs was sonicated using Diagenode Bioruptor Plus in 15 ml Diagenode Falcon tubes, cell lysates incubated with corresponding antibody over night at 4°C and Dynabeads were added the next day. In case of Bio-Ehmt1 and corresponding inputs, DNA was digested with Micrococcal Nuclease (Cell Signaling) and incubated with M-280 Streptavidin coupled Dynabeads (Invitrogen) for 1h at 4°C. Beads were washed, eluted and the suspension was de-crosslinked over night at 65 °C. DNA of ChIPs from endogenous proteins and corresponding inputs was purified using MinElute PCR Purification Kit (QIAGEN) and of Bio-Ehmt1 ChIPs and corresponding inputs using AMPure XP beads (Beckman Coulter). ChIP-seq libraries were prepared using NEBNext Ultra kit (New England BioLabs) following the manufacturer's recommendations.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
66441482
Reads aligned (%)
96.2
Duplicates removed (%)
11.9
Number of peaks
505 (qval < 1E-05)

mm9

Number of total reads
66441482
Reads aligned (%)
96.0
Duplicates removed (%)
11.9
Number of peaks
618 (qval < 1E-05)

Base call quality data from DBCLS SRA