Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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
embryonic fibroblasts, E13.5
strain
mixed
cell type
3T9 fibroblasts
genotype/variation
c-mycflox/flox; in vitro infected with MycER
chip antibody
H3K4me1 (Abcam, catalog# ab8895, lot# GR46388-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42330051
Reads aligned (%)
95.7
Duplicates removed (%)
10.3
Number of peaks
81218 (qval < 1E-05)

mm9

Number of total reads
42330051
Reads aligned (%)
95.7
Duplicates removed (%)
10.3
Number of peaks
81203 (qval < 1E-05)

Base call quality data from DBCLS SRA