Illumina HiSeq 2000 sequencing; Otx2 binding to Nanog promoter protects embryonal stem cells from corruption of naive pluripotency and is required at morula stage for inner-cell mass differentiation of the epiblast
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Embryo
Cell type
Epiblast
NA
NA
Attributes by original data submitter
Sample
ENA first public
2016-06-09
ENA last update
2018-03-09
ENA-CHECKLIST
ERC000011
External Id
SAMEA3522257
INSDC center alias
Telethon Institute of Genetics and Medicine (Tigem)
INSDC center name
Telethon Institute of Genetics and Medicine (Tigem)
INSDC first public
2016-06-09T17:01:07Z
INSDC last update
2018-03-09T04:17:36Z
INSDC status
public
Submitter Id
E-MTAB-3856:EPISC_WT2
broker name
ArrayExpress
cell line
embryonic cell line
cell type
epiblast cell
common name
house mouse
genotype
wild type genotype
sample name
E-MTAB-3856:EPISC_WT2
Sequenced DNA Library
library_name
EPISC_WT2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-assay were performed from 10e7 cells per experiment. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Glycine at a final concentration of 0.125 M was added to quench the reaction. Cells were collected and lysed in SDS buffer and chromatin was then sonicated to an average size of 0,2-0,3 kb. After a 30 minute step of chromatin preclearing with the Protein A Agarose/Salmon Sperm DNA 50% gel slurry (Millipore), rabbit polyclonal antibody against Otx2 was added to the chromatin and incubated overnight at 4°C. The immunoprecipitated complex was subsequently incubated with the Protein A Agarose for 2-4 hours at 4°C. Agarose beads were then washed, chromatin was eluted and reverse-crosslinked overnight at 65°C. EpiSCs were induced from ESCs on serum-coated dishes in N2B27 medium supplemented with activin A and Fgf2. Proteinase K treatment and phenol/chloroform purification. Libraries were prepared according to Illumina standard protocols with internal barcodes.