Difference between revisions of "WBConfCall 2019.11.21-Agenda and Minutes"

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== Allele CRISPR Nomenclature ==
== Allele CRISPR Nomenclature ==
* [https://github.com/WormBase/website/issues/7400 I had a question regarding C. elegans genetic nome... #7400]
Two questions have been asked recently:
Two questions have been asked recently:

Revision as of 14:09, 21 November 2019


Open Tickets

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

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:

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 transgene describing the additional mutation that has been added to the original kcIs40[ifp-1p::ifp-1::egfp]IV) transgene.