Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
EpiSC
NA
NA

Attributes by original data submitter

Sample

source_name
EpiSC/MM401-H3K4me1-ChIP-seq
cell type
EpiSC treated by MM401
genotype
CD1/JF1
chip antibody
H3K4me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP experiments were performed using 3E6 cells and 4µg a-Mll1 antibody per ChIP (5E7 cells in total) ; 2.5ug a-H3K4me1 and 2.5ug H3K4me3 antibody per ChIP according to standard protocols. For Mll1-ChIP, crosslinking of the cells was performed with dimethyl pimelimidate dihydrochloride (DMP, Sigma-D8388) on the culture plates for 30 minutes. While ChIPed DNA was collected and purified by Qiaquick PCR purification Kit (Qiagen). Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
49982980
Reads aligned (%)
90.2
Duplicates removed (%)
13.1
Number of peaks
721 (qval < 1E-05)

mm9

Number of total reads
49982980
Reads aligned (%)
90.1
Duplicates removed (%)
13.1
Number of peaks
892 (qval < 1E-05)

Base call quality data from DBCLS SRA