Antigen

Antigen Class

Input control

Antigen

Input control

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

Embryoid Bodies

strain/background

129/C57Bl/6/ICR

genotype/variation

WT

cell type

Embryoid Bodies

chip type

native

chip antibody

none

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with MNase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cells were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina TruSeq protocol.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

72516125

Reads aligned (%)

98.7

Duplicates removed (%)

12.3

Number of peaks

203 (qval < 1E-05)

mm9

Number of total reads

72516125

Reads aligned (%)

98.6

Duplicates removed (%)

12.7

Number of peaks

192 (qval < 1E-05)