characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-07-18T17:02:35Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-14T10:49:50Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104212303
characteristics.characteristic: External Id
characteristics.text: Cancer Research UK - Cambridge Institute (CRUK-CI) and Department of Chemistry, University of Cambridge, UK
characteristics.characteristic: INSDC center name
characteristics.text: 2018-07-18T17:02:35Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-14T10:49:50Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1871321
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5960:RNA_Heart_KO2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: TDG KO mice generation protocol: The Tdg-targeting construct (Supplementary Fig. 1) was generated by replacement of a NarI-PacI fragment enclosing exons 6 and 7 by a neomycin resistance cassette in a cloned fragment spanning exons 5-10 of the Tdg locus. This construct was used to target the Tdg allele in 129 mouse ESCs, which were then used to generate chimaeras and, ultimately, Tdg+/− heterozygotes by backcrossing to C57BL/6. Text taken from: doi:10.1038/nature09672 Breeding and tissue collection: Mice were maintained as heterozygotes and intercrossed to generate homozygous knockout embryos for analysis. Tissues were collected from timed matings with the day of the copulation plug as E0.5. Embryos were dissected into hindbrain, heart, liver and carcass.Text taken from: https://doi.org/10.1186/s13059-016-1001-5. NaBH4 was used to reduce 5-fC to 5-hmC as a control in the nucleosome reconstitution experiment (SLX-11454* samples) to demonstrate that MNase signal is derived from 5-fC. More details can be found in our previous work<http://www.nature.com/nchem/journal/v6/n5/full/nchem.1893.html>. NaBH3CN is a reducing agent which irreversibly traps out the Schiff base interactions (covalent bonds) between 5-fC and histone proteins. It was used in the polymerase stop assays (Polstop* samples). The concentration of NaBH3CN used was 100mM, the concentration where we had observed DNA-histone subunit cross-linking by gel electrophoresis. Genomic DNA and RNA was extracted from mouse embryonic tissues using the DNeasy Blood & Tissue kit (Qiagen). DNA library preparation for sequencing was done using the NEBNext DNA library preparation kit (New England Biolabs Inc.)
characteristics.characteristic: description
characteristics.text: embryonic day 11.5
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002562
characteristics.characteristic: developmental stage
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: 2
characteristics.characteristic: replicate
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: RNA_Heart_KO2
characteristics.characteristic: title