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 embroid bodies
cell line
Mouse ES cells
genetic background
C57BL/6J
genotype
wild type
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-Seq samples, 2 million ES or EB cells were collected at the indicated time point and extracted with PrepEase RNA spin kit (Affymetrix). For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB431542 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis. For RNA-Seq library construction, total RNA purified from mES and mEB was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions. For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions. Multiplexed sequencing libraries were ran on a Hiseq2500 platform and more than 40million raw paired-end reads were generated for each sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
24219297
Reads aligned (%)
96.3
Duplicates removed (%)
5.7
Number of peaks
268 (qval < 1E-05)

mm9

Number of total reads
24219297
Reads aligned (%)
96.2
Duplicates removed (%)
6.4
Number of peaks
248 (qval < 1E-05)

Base call quality data from DBCLS SRA