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The Ontology for Biomedical Investigations
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NTR: sequencing assays #1457

Open patrick-lloyd-ray opened 3 years ago

patrick-lloyd-ray commented 3 years ago

patch-seq assay

Label: patch-seq assay Alternative term(s): patch clamp and RNA sequencing assay Definition: A single-cell RNA sequencing assay that takes a patch clamp recording from a cell and then uses the intracellular content aspirated into the pipette for downstream RNA-sequencing. Definition source: http://doi.org/10.1038/nprot.2017.120 Parent class: single-cell RNA sequencing assay
xref: EFO:0008853

dropseq

Label: droplet-based single-cell RNA sequencing assay Alternative term(s): Dropseq Definition: A single-cell RNA sequencing assay that analyzes mRNA transcripts from droplets of individual cells. The droplets are compartmentalized via a microfluidic device. After the cells are compartmentalized, cells in droplets are lysed and the released mRNA hybridizes to the oligo(dT) tract of the primer beads. Then the droplets are pooled and broken to release the beads which are then isolated and reverse-transcribed with template switching. The resulting cDNA strands are PCR-amplified and the sequencing adapters are added. The barcoded mRNA samples are then sequenced. Definition source: https://doi.org/10.1016/j.cell.2015.05.002 Parent class: single-cell RNA sequencing assay xref: EFO:0008722

SNARE-seq2

Label: single-nucleus chromatin accessibility and mRNA expression sequencing assay Alternative term(s): SNARE-seq2 Definition: A sequencing assay that generates a library of cDNA and open chromatin gDNA fragments by tagmenting a single nuclei and open chromatin, and encapsulating those in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead which capture both mRNAs and open chromatin fragments. Definition source: https://doi.org/10.1038/s12276-020-0420-2 Parent class: sequencing assay Note: the evaluant of this assay is a nucleus specimen (or single nucleus specimen) and may require a new ‘nucleus specimen’ or ‘single nucleus specimen’ term added.

SMARTseq

Label: switching mechanism at the 5’ end of RNA template assay Alternative term(s): SMARTseq Definition: A single cell sequencing assay wherein cells are lysed and their recovered RNA is hybridized to an oligo(dT) that primes a reverse transcription reaction, the outcome of which are cDNA’s that have PCR handles on both ends. The cDNA's are then amplified using PCR, and the products are sequenced. Definition source: http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/ Parent class: single-cell RNA sequencing assay xref: EFO:0008930

SMARTseq2

Label: switching mechanism at the 5’ end of RNA template assay 2 Alternative term(s): SMARTseq2 Definition: A switching mechanism at the 5' end of RNA template sequencing assay that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. Definition source: https://doi.org/10.1038/nprot.2014.006 Xref: SMARTseq (new term from above)

Notes

Some axioms should be added as well, which are documented here. I'm happy to discuss these on an OBI call. Thanks!

hectorguzor commented 3 years ago

Hi @patrick-lloyd-ray

I was asked to review some assays for issue #1393 and noticed that her team is also working on a term for 'single-nucleus chromatin accessibility and mRNA expression sequencing assay'. Perhaps you can look at that one and we can discuss it on 2021-11-22 in the OBI call. @mgiglio99 can you look at Patrick's assay.

patrick-lloyd-ray commented 3 years ago

Thanks, @hectorguzor.

I believe that the assays are distinct as SNAREseq2 is a version of SNAREseq. In https://doi.org/10.1038/s41596-021-00507-3 the authors state:

Because the community is moving toward the generation of multi-omics cell maps on various organs and tissues, a method with a higher scalability [than SNAREseq] and comparable data quality is desirable. Here, we present an improved protocol, called ‘SNARE-seq2’, that uses combinatorial indexing to increase the throughput by 10- to 100-fold and permits processing of multiple samples in the same batch to reduce technical variations.

I think the distinction is captured by the definitions, but I'm happy to amend what I've written based on input from the group. Perhaps we could also add some additional metadata so that users are not confused.

Here is a protocols.io doi: https://doi.org/10.17504/protocols.io.be5gjg3w

And here is the doi for the relevant publication I'm working from: https://doi.org/10.1101/2020.03.31.016972

mgiglio99 commented 3 years ago

Thanks all, So, based on above statement that SNARseq2 is a version of SNARseq, then I take it that the SNARseq2 term will become a child of our new SNAREseq term. Therefore, the definition above could be revised to "A SNAREseq assay that generates...." Is that consistent with what you were thinking? Michelle

DanBerrios commented 3 years ago

The Drop-seq paper refers to the assay with a hyphen (not Dropseq). Should we also?

patrick-lloyd-ray commented 3 years ago

@DanBerrios Yes, thank you!

hectorguzor commented 3 years ago

Discussed on OBI call 2021-11-22:

mgiglio99 commented 6 months ago

Further discussion on May 13, 2024 meeting. Decided that Smartseq and Smartseq2 should be sibs of each other same with Snareseq and Snareseq2. If there ends up being a lot of versions of any of these assays, we can explore creation of a grouping parent term for them as needed.

We will also follow up with Patrick to restart the pull request process on this.

mgiglio99 commented 4 months ago

@patrick-lloyd-ray Sorry for the delay on this one. Is this still something you're interested in? If so, can you start a new pull request based on the final comment above from May?

patrick-lloyd-ray commented 4 months ago

Yes, sorry, this dropped off my priorities list for a moment. I will take a look this week.

mgiglio99 commented 4 months ago

Hi Patrick - no rush : )

mgiglio99 commented 1 month ago

Hi Patrick, Sorry to bug you - just checking in on this one. Thanks, Michelle