McClean: Yeast Nomenclature: Difference between revisions
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==Overview== | ==Overview== | ||
'S. cerevisiae' researchers have a systematic approach for describing genotypes of yeast strains. | ''S. cerevisiae'' researchers have a systematic approach for describing genotypes of yeast strains. We need to follow this system when writing papers, protocols, and when entering yeast strains into the lab database. | ||
Yeast nomenclature is covered well in the articles listed in the references, so I won't recapitulate all of the details here. You should refer to these references when you have questions. I will just list some of the common conventions that you might need when entering strains into the lab database. | |||
==Nomenclature== | ==Nomenclature== | ||
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===Genetic Background=== | ===Genetic Background=== | ||
===Alleles=== | |||
====Alleles created by recombinant DNA technology==== | |||
# '''Disruptions''' | |||
# '''Deletions''' | |||
#* Deletions are written as the name of the gene that is altered following by -Δ; for example arg2-Δ1, where the number 1 denotes a specific complete or partial deletion of arg2. | |||
#'''Replacements''' | |||
#* Replacements should be written as the name of the gene that is replaced followed by the symbole Δ::. Examples: | |||
#** If you deleted the entire open reading frame of the GAL1 gene with a drug resistance cassette (such as NatMX for ClonNat resistance) you would write gal1Δ::NatMX. | |||
#**If you deleted the GAl1 open reading frame with a fluorescent reporter (for instance, with GFP-KanMX if you wanted a quick reporter of P<sub>GAL1</sub> promoter activity) you would write the genotype as ga1Δ::GFP-KanMX | |||
==Notes== | ==Notes== | ||
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Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip. | Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip. | ||
'''*[[User:Megan N McClean|Megan N McClean]] 11:29, 16 November 2012 (EST)''':I got some helpful tips from P. Gibney on how he writes out promoter replacements: | |||
* YFG(-1 to -n)Δ::KanMX-GAL1(-1 to -n) | |||
* YFGprΔ::KanMX-GAL1pr | |||
So far as we could figure out there is no perfect/official way to do it, but this notation gives you a clear idea of what was done. Especially the detailed YFG(-1 to -n) notation which tells you which part of the promoter was actually replaced with which part of the GAL1 promoter. | |||
==References== | ==References== | ||
Burke, D. Dawson, D. & Sterns, T. 2000 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual ''Cold Spring Harbor Laboratory Press'' | |||
Sherman, F. 2002 Getting started with yeast ''Methods Enzymol'', 350, 3-41 | |||
[http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf ''Saccharomyces cerevisiae'' Genetic Nomenclature Guide] | |||
==Contact== | ==Contact== | ||
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Latest revision as of 09:30, 16 November 2012
Overview
S. cerevisiae researchers have a systematic approach for describing genotypes of yeast strains. We need to follow this system when writing papers, protocols, and when entering yeast strains into the lab database.
Yeast nomenclature is covered well in the articles listed in the references, so I won't recapitulate all of the details here. You should refer to these references when you have questions. I will just list some of the common conventions that you might need when entering strains into the lab database.
Nomenclature
Chromosomal Genes
Nonmendelian Determinants
Genetic Background
Alleles
Alleles created by recombinant DNA technology
- Disruptions
- Deletions
- Deletions are written as the name of the gene that is altered following by -Δ; for example arg2-Δ1, where the number 1 denotes a specific complete or partial deletion of arg2.
- Replacements
- Replacements should be written as the name of the gene that is replaced followed by the symbole Δ::. Examples:
- If you deleted the entire open reading frame of the GAL1 gene with a drug resistance cassette (such as NatMX for ClonNat resistance) you would write gal1Δ::NatMX.
- If you deleted the GAl1 open reading frame with a fluorescent reporter (for instance, with GFP-KanMX if you wanted a quick reporter of PGAL1 promoter activity) you would write the genotype as ga1Δ::GFP-KanMX
- Replacements should be written as the name of the gene that is replaced followed by the symbole Δ::. Examples:
Notes
Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!
- List troubleshooting tips here.
- You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
- Anecdotal observations that might be of use to others can also be posted here.
Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.
*Megan N McClean 11:29, 16 November 2012 (EST):I got some helpful tips from P. Gibney on how he writes out promoter replacements:
- YFG(-1 to -n)Δ::KanMX-GAL1(-1 to -n)
- YFGprΔ::KanMX-GAL1pr
So far as we could figure out there is no perfect/official way to do it, but this notation gives you a clear idea of what was done. Especially the detailed YFG(-1 to -n) notation which tells you which part of the promoter was actually replaced with which part of the GAL1 promoter.
References
Burke, D. Dawson, D. & Sterns, T. 2000 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual Cold Spring Harbor Laboratory Press
Sherman, F. 2002 Getting started with yeast Methods Enzymol, 350, 3-41
Saccharomyces cerevisiae Genetic Nomenclature Guide
Contact
- Megan N McClean 14:01, 4 June 2012 (EDT)
or instead, discuss this protocol.
