characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-08-01T00:24:07Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-08-01T00:24:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10106922
characteristics.characteristic: External Id
characteristics.text: BioSysM - LMU Munich
characteristics.characteristic: INSDC center name
characteristics.text: 2022-08-01T00:24:07Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-08-01T00:24:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS7763543
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-10933:WT_r1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: J1
characteristics.characteristic: cell line
characteristics.text: mouse embryonic stem cell
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Three cell lines (WT J1, Tet1 KO H9 and Tet1 CM D7) were cultured as independent triplicates. The generation of Tet1 KO (clone H9) and Tet1 CM (clone D7) mESC lines was described previously (18, 30). Mouse ESCs were cultured in “Serum LIF” conditions and as independent replicates for 6 days prior to experiments. Here the cells were maintained on 0.2% gelatin-coated dishes in Dulbecco's modified Eagle's medium (Sigma) supplemented with 16% fetal bovine serum (FBS, Sigma), 0.1 mM ß-mercaptoethanol (Invitrogen), 2 mM L-glutamine (Sigma), 1× MEM Non-essential amino acids (Sigma), 100 U/mL penicillin, 100 μg/mL streptomycin (Sigma), LIF (ESGRO, Millipore). The genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGEN). DNA concentration was measured using Nanodrop (NanoPhotometer NP80, Implen). The gDNA was then diluted to 10ng/µL in 200µL TE buffer. To control the conversion efficiency 0,01 ng pUC19 methylated DNA and 0,2 ng unmethylated lambda DNA were added. The DNA was sheared into 350 - 400 bp fragments using the Bioruptor Plus sonication device (Diagenode) (30s on/off, 20 cycles). Bioanalyzer (Agilent) was used to control for the shearing efficiency. For library preparation 200 ng of the sheared DNA were used. The final EM-seq library preparation was performed according to the manufacturer's instructions (New England Biolabs).
characteristics.characteristic: description
characteristics.text: mouse embryo stage
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: blastocyst
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: 129S4/SvJae
characteristics.characteristic: strain
characteristics.text: WT_r1
characteristics.characteristic: title