Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
Mouse embryonic fibroblasts
genotype
Rnf40+/+
passages
3
chip antibody
H3K27me3 (Diagenode, pAb-195-050)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose. Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
31078359
Reads aligned (%)
95.1
Duplicates removed (%)
4.0
Number of peaks
1156 (qval < 1E-05)

mm9

Number of total reads
31078359
Reads aligned (%)
95.0
Duplicates removed (%)
4.0
Number of peaks
1160 (qval < 1E-05)

Base call quality data from DBCLS SRA