WBConfCall 2019.11.21-Agenda and Minutes
- Request: Import single cell transcription profiling experiment data #7432
- WormBase BLAST no longer provides links to gene/protein #7435
- Cannot watch video in Wormbook #7392 (was to be forwarded to WormBook, as discussed two weeks ago)
- Changes to your links display on Europe PMC website (from Dayane Araújo, Technical Outreach Officer, Europe PMC)
Moving to Zoom platform from GOTO meeting starting December
- GOTO meeting hiccups happened a few times. Helpless customer support experience.
- AGR uses Zoom with good experience.
WormCat - Amy Walker Lab
- Tool for RNA seq visualizaton #7436 Gene Set Enrichment WormCat
Categories of mixed aspects: Cat1 like "Neuronal function"; "Non-coding RNA", Cat3 "Peroxisome: other", "Signaling: Janus" each has member of one gene Difficult to update 'Curated' Categories (34 Cat1(248 Cat2(455 Cat3))) One gene - one Category ONLY: lin-3 "Development: general"; let-23 "Signaling: Y kinase" Suggested link under Resources:External databases https://wormbase.org/resources#3--10
Allele CRISPR Nomenclature
Two questions have been asked recently:
C. elegans genetic nomenclature upon CRISPR. If I make one modification using CRISPR (e.g. bus-50(e5000), and in a separate experiment modify bus-50(e5000) to create another lesion elsewhere in the gene, would it be bus-50(e5000e5001) or would it be bus-50(e5002).
Tim S. Comments -- The second lesion would be e5001; putting it in the order e5000e5001 helps the reader know that this change was added to the e5000 allele. Once the author explains what bus-50(e5000e5001) is, then they can use bus-50(e5001) for short.
In the million mutation project, different alleles in one gene are labelled as a list of alleles. Furthermore, revertants are labelled as shown- lin-12(n676n930)-n930 is an intragenic revertant of the n676 lin-12 gain of function allele.
- Would we do something similar to the Cis double mutants (curate e5000 and e5001 but then link them via (e5000e5001) Allele). I'm not sure about the intragenic revertant alleles.
Tim S. Comments: -- Yes. Intragenic revertants would get an new allele name, e5002
2) Personal email: By microinjection and subsequent integration we generated an “Is” transgene (in our case kcIs40[ifp-1p::ifp-1::egfp]IV). Subsequently, this integrated sequence was mutated by CRISPR/cas together with the endogenous ifp-1 gene. The mutated endogenous gene (in our case ifp-1) was named “ifp-1(kc18)” but we are at a loss how to name the mutated “kcIs40” locus. Is it a transgene (new kcIs) or a new ifp-1 allele (new kc)?
- Instinctively I would suggest creating a new kcIs transgene describing the additional mutation that has been added to the original kcIs40[ifp-1p::ifp-1::egfp]IV) transgene.
Tim S. Comments: -- Yes, I think it makes most sense if this just gets a new Is name.
Moving from GoTo Meeting to Zoom
- will happen in December and Raymond will update the mails
- will be for the WormBase conference calls
- EuropePMC update will probably not affect us
- WormBook (Daniel will look into it and contact Todd. If needed we could offload it to NCBI)
- Blast Interface links to hits is being looked into by OICR
- there is a rotation student at CalTech who could look into the display/analysis of the single-cell expression data
- clustering could be redone regularly if needed
- could be of interest for AGR
- Raymond added some comments above
- will it be updated?
- has some custom ontology rather than GO
- Todd proposed that we could collect/host a selection of tools as part for AGR (using some standard containers)
- investigate a bit more
- add a link
- ask them to containerise their software
- Paul proposed to create bridging objects to link transgenes to variations if needed
- Tim proposed to create new transgene/allele objects for the mutated crispers
- upload is this Friday
- any news for the release notes should be sent to Paul