Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

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

Attributes by original data submitter

Sample

source_name
Embryonic stem cells
cell line
SEES-3
chip antibody
H3K4me3 (Millipore, 07-473)
treatment
Doxycycline (1 ug/ml)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. The ChIPed DNA libraries were constructed using NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB).

Sequencing Platform

instrument_model
Illumina MiSeq

hg38

Number of total reads
2745224
Reads aligned (%)
98.9
Duplicates removed (%)
0.7
Number of peaks
6012 (qval < 1E-05)

hg19

Number of total reads
2745224
Reads aligned (%)
98.1
Duplicates removed (%)
1.2
Number of peaks
6005 (qval < 1E-05)

Base call quality data from DBCLS SRA