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)
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 answered recently and we will be discussing things this afternoon in our call and I wondered if you had any ideas on setting up additional standards:
1) 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). 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.
2) 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 describing the additional mutation that has been added to the original kcIs40[ifp-1p::ifp-1::egfp]IV) transgene.