Antigen

Antigen Class

TFs and others

Antigen

Smad3

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 body

cell line

E14Tg2a.IV

chip antibody

Smad3 (Cell Signaling Technology, 9523S)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIPseq, Lysates were clarified from sonicated cells and transcription factor-DNA complexes were isolated with antibody. For RNAseq, PrepEase RNA Spin Kit (Affymetrix) were used for RNA extraction.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

106950075

Reads aligned (%)

89.7

Duplicates removed (%)

22.4

Number of peaks

27285 (qval < 1E-05)

mm9

Number of total reads

106950075

Reads aligned (%)

89.5

Duplicates removed (%)

22.9

Number of peaks

27311 (qval < 1E-05)