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

EB

cell type

EB

replicate

replicate1

antibody

Input

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Nuclei were isolated, mononucleosomes were subsequently obtained from CCE mESCs and CCE EBs. Cells were lysed in hypotonic TMSD buffer to isolate nuclei, which were then digested with micrococcal nuclease. The resulting mononucleosomes were immunoprecipitated with Protein AG beads (Pierce) bound to either anti-Brd4 (Abcam) or anti-acetyl-H4 (Millipore). Washed beads from ChIP were then treated with RNase A followed by Proteinase K. Samples were cleaned up using DNA Clean & Concentrator-5 (Zymogen) The ChIP library was prepared using the multiplexed ChIP-Seq sample preparation protocol available on the University of Pennsylvania Functional Genomics Core website (http://fgc.genomics.upenn.edu/) anti-Brd4 (Abcam 128874 and anti-acetyl-H4 (Millipore 06-866)

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

78596921

Reads aligned (%)

94.5

Duplicates removed (%)

40.2

Number of peaks

436 (qval < 1E-05)

mm9

Number of total reads

78596921

Reads aligned (%)

94.3

Duplicates removed (%)

40.2

Number of peaks

446 (qval < 1E-05)