characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-09-30T04:05:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2019-10-21T13:50:46Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA6104600
characteristics.characteristic: External Id
characteristics.text: Faculty of Biology Department II Ludwig Maximilians University Munich
characteristics.characteristic: INSDC center name
characteristics.text: 2020-09-30T04:05:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2019-10-21T13:50:46Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS3905281
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6785:wt_ESC_RRBS_rep1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: J1
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004990
characteristics.characteristic: cell line
characteristics.text: embryonic stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002322
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were collected by trypsinization Naïve J1 mouse ESCs were cultured and differentiated into EpiLCs as described previously (Hayashi and Saitou, 2013; Mulholland et al., 2015). In brief, for both naïve ESCs and EpiLCs defined media was used, consisting of N2B27: 50% neurobasal medium (Life Technologies), 50% DMEM/F12 (Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM β-mercaptoethanol (Life Technologies), N2 supplement (Life Technologies), B27 serum-free supplement (Life Technologies), 100 U/mL penicillin, and 100 μg/mL streptomycin (Sigma). Naïve ESCs were maintained on flasks treated with 0.2% gelatin in defined media containing 2i (1 μM PD032591 and 3 μM CHIR99021 (Axon Medchem, Netherlands)), 1000 U/mL recombinant leukemia inhibitory factor (LIF, Millipore), and 0.3% BSA (Gibco) for at least three passages before commencing differentiation. For reprogramming experiments, naive media was supplemented with freshly prepared 100 µM Vitamin C (L-ascorbic acid 2-phosphate, Sigma). Column purification For RRBS, genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGEN), after an overnight lysis and proteinase K treatment. RRBS library preparation was performed as described previously (Boyle et al. 2012), with the following differences: bisulfite treatment was performed using the EZ DNA Methylation-Gold™ Kit (Zymo Research Corporation) according to the manufacturer's protocol.
characteristics.characteristic: description
characteristics.text: blastocyst
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000358
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: inner cell mass
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000087
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: wt_ESC_RRBS_rep1
characteristics.characteristic: title