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
Pluripotent stem cell
Cell type
ES cells
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
SAMEA3522261
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
2018-03-09T03:28:22Z
INSDC status
public
Submitter Id
E-MTAB-3856:ESC_WT2
broker name
ArrayExpress
cell line
embryonic cell line
cell type
embryonic stem cell
common name
house mouse
genotype
wild type genotype
sample name
E-MTAB-3856:ESC_WT2
Sequenced DNA Library
library_name
ESC_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. E14Tg2a wt and Obs3 mutant ESCs were routinely grown in GMEM medium plus 12% FBS (Hyclone) and LIF (Millipore). Proteinase K treatment and phenol/chloroform purification. Libraries were prepared according to Illumina standard protocols with internal barcodes.