Sample information curated by ChIP-Atlas

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.

Attributes by original data submitter

Sample

source_name
mouse embryonic stem cell
chip antibody
input
genotype
MLL3-/-;MLL4flox/flox
cell type
Differentiated embryoid body at day 4
genetic background
C57BL/6 and SV/129

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, suspended 10 x 106 ESCs (feeder removed) and EBs are fixed with 1% formaldehyde in culture medium, followed by ChIP assay. For RNA-Seq, total RNA are collected using Trizol extraction followed by mRNA purification using Dynabeads® mRNA DIRECT™ Kit (invitrogen). Libraries were prepared according to Illumina TruSeq RNA and DNA sample preparation Kit

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
44948341
Reads aligned (%)
73.7
Duplicates removed (%)
11.9
Number of peaks
440 (qval < 1E-05)

mm9

Number of total reads
44948341
Reads aligned (%)
73.6
Duplicates removed (%)
11.9
Number of peaks
477 (qval < 1E-05)

Base call quality data from DBCLS SRA