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

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* Blast Interface links to hits is being looked into by OICR
 
* 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
 
* there is a rotation student at CalTech who could look into the display/analysis of the single-cell expression data
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== WormCat ==
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== Crisper Nomenclature ==

Revision as of 16:45, 21 November 2019

Agenda

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) I had a question regarding C. elegans genetic nome... #7400

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.

Minutes

Moving from GoTo Meeting to Zoom

will happen in December and Raymond will update the mails

Open Tickets

  • 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

WormCat

Crisper Nomenclature

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