Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Pluripotent stem cell

Cell type

ES cells

NA

NA

Sample

source_name

WT_mES_H3K4me3

strain

R1 129/Sv

genotype/variation

WT

cell type

mESC

chip-antibody

Homemade

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

Sequencing Platform

instrument_model

HiSeq X Ten

mm10

Number of total reads

17701523

Reads aligned (%)

89.4

Duplicates removed (%)

12.2

Number of peaks

28240 (qval < 1E-05)

mm9

Number of total reads

17701523

Reads aligned (%)

89.3

Duplicates removed (%)

12.1

Number of peaks

28198 (qval < 1E-05)