Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
EpiSC
NA
NA

Attributes by original data submitter

Sample

source_name
EpiSC-H3K4me3
cell type
Epiblast stem cells
chip antibody
H3K4me3 (Abcam,ab8580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were collected and fixed in 1% formaldehyde solution and quenched by 0.125M glycine. Fixed cells were fragmented to a size range of 200-500bp by using Bioruptor Pico. Solubilized fragmented chromatin was immunoprecipitated with antibodies.Fragmented DNA was extracted with phenol-chloroform and precipitated with ethanol DNA fragments acquired from immunoprecipitation would be subjected to end-repaired, adaptor ligation and PCR amplification under the instruction of the manufacturers (New England Biolabs E7370 ).

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
15529435
Reads aligned (%)
97.8
Duplicates removed (%)
11.9
Number of peaks
19651 (qval < 1E-05)

mm9

Number of total reads
15529435
Reads aligned (%)
97.7
Duplicates removed (%)
11.9
Number of peaks
19634 (qval < 1E-05)

Base call quality data from DBCLS SRA