characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-07-29T00:19:20Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-07-29T00:19:20Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10107497
characteristics.characteristic: External Id
characteristics.text: BioSysM - LMU Munich
characteristics.characteristic: INSDC center name
characteristics.text: 2022-07-29T00:19:20Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-07-29T00:19:20Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS7764057
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-10937:TET1KO_r3
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: For RNA-seq, three different cell lines (WT J1, Tet1 KO H9, Tet1 CM D7) were cultured as independent quadruplicates. 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). RNA was isolated using the NucleoSpin Triprep Kit (Machery-Nagel) according to the manufacturer’s instructions. Isolated total RNA was normalised and subjected to RNA sequencing using a version of the prime-seq method (https://www.protocols.io/view/prime-seq-s9veh66). This method is based on the single cell RNA-seq method mcSCRB-seq (90) and is a three prime counting method that includes a sample specific barcode sequence (see scan name) and unique molecular identifiers (UMI) for accurate quantification of gene expression. Here we used the Nextera XT Kit (Illumina) for sequencing library preparation as described in the mcSCRB-seq protocol (90).
characteristics.characteristic: description
characteristics.text: mouse embryo stage
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: TET1 knockout
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: TET1KO_r3
characteristics.characteristic: title