Antigen

Antigen Class

Histone

Antigen

H4K20me3

Cell type

Cell type Class

Pluripotent stem cell

Cell type

Embryoid Bodies

MeSH Description

Spontaneous aggregations of human embryonic stem cells that occur in vitro after culturing in a medium that lacks LEUKEMIC INHIBITORY FACTOR. The embryoid bodies can further differentiate into cells that represent different lineages.

Sample

source_name

shSmyd5_EB

genotype/variation

Smyd5 depletion

cell type

embryoid body (EB)

chip antibody

Anti-H4K20me3 (Abcam; ab9053)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays. ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

18065708

Reads aligned (%)

96.1

Duplicates removed (%)

39.9

Number of peaks

587 (qval < 1E-05)

mm9

Number of total reads

18065708

Reads aligned (%)

95.3

Duplicates removed (%)

39.8

Number of peaks

637 (qval < 1E-05)