NTR: single-nucleus methylcytosine and transcriptome sequencing assay

[jenjou]

Preferred Term: single-nucleus methylcytosine and transcriptome sequencing assay Synonyms: snmCT-seq Definition: A multiomic method to measure the cytosine DNA methylation and gene expression signature of single cells. Relevant info: https://www.biorxiv.org/content/10.1101/434845v1 Parent Term: OBI:0001177 (RNA sequencing assay) and OBI:0001266 (DNA methylation profiling by high throughput sequencing assay)

[DanBerrios]

We are the process of re-organizing our sequencing-related assays. We could add this term sooner rather than later, but its placement in the ontology could shift later as a result. @jenjou Would you prefer us to wait until that reorg is done, or do you need this term more urgently? @jenjou

[jenjou]

I think having an official OBI term ID is more important to us than its exact placement within the ontology. However, we (IGVF Consortium) have set up a placeholder for internal use in the meantime, so we can wait as needed. If it would make your development process easier to complete the reorganization before adding new terms, that seems OK with me.

[bpeters42]

Discussed on 7/8 call; let's try to create a class and then re-arrange it with everything else. @jenjou to clarify single nucleus vs. cell and update definition.

[jenjou]

I think there was some confusion on my part, since the linked Biorxiv preprint describes both a single cell and single nucleus version of the assay. Here I would just like to request the single nucleus type for now, so I would change the description to:

A multiomic method to measure the cytosine DNA methylation and gene expression signature of single nuclei.

[DanBerrios]

For the snmCT assay, the input is both nuclear DNA and RNA. (Same for scmCT, input is both cellular DNA and RNA). We discussed that we should declare the parent to be DNA methylation profiling by high throughput sequencing assay, but also add an axiom to have it inferred as a child of RNA-seq/transcriptome profiling assay.