Cryptococcus at the FGSC
Deletion Sets
Please note that the FGSC cannot break up sets of arrayed mutants. You should request an entire set as described below, or request individual clones (please send plate and well location).
FGSC has not independently verified phenotypes or genotypes of any of the strains in the deletion sets. Questions about these mutants should be sent directly to the depositor.
2007 J. Lodge: Strains at the FGSC in 2 plates (A and B),
Not all strains listed in background data were sent to the FGSC.
Genetic (DNA and protein sequence data), quality control data (Southern blot data), and phenomic data for mutants are available for transcription factors, kinases and phosphatases.
2015 Bahn set of 4 plates (MS Excel)
Available as a complete set of four plates or as individual clones.
This set is all of kinase deletion mutants.
Please see Jung KW, Yang DH, Maeng S, Lee KT, So YS, et al. (2015) Systematic functional profiling of transcription factor networks in Cryptococcus neoformans. Nat Comms 6: 6757.
http://www.ncbi.nlm.nih.gov/pubmed/25849373
2016 Bahn set of 5 plates (MS Excel)
Available as a complete set of five plates or as individual clones.
This set is all of kinase deletion mutants.
Please see Lee, Kyung-Tae, et al. "Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans." Nature Communications 7 (2016).
https://www.ncbi.nlm.nih.gov/pubmed/27677328
Received in November 2016.
2020 Bahn set of 3 plates (MS Excel)
Available as a complete set of five plates or as individual clones.
This set is all of phosphatase deletion mutants.
Please see Jin JH, Lee KT, Hong J, Lee D, Jang EH, Kim JY, Lee Y, Lee SH, So YS, Jung KW, Lee DG, Jeong E, Lee M, Jang YB, Choi Y, Lee MH, Kim JS, Yu SR, Choi JT, La JW, Choi H, Kim SW, Seo KJ, Lee Y, Thak EJ, Choi J, Averette AF, Lee YH, Heitman J, Kang HA, Cheong E, Bahn YS. 2020. Genome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans. Nature Communications 11(1):4212. doi: 10.1038/s41467-020-18028-0. PMID: 32839469; PMCID: PMC7445287.
Received July 2020.
Individuals interested in performing systematic, high-throughput analysis are asked to contact the Madhani lab to ensure coordination with ongoing efforts (hitenmadhani@gmail.com).
Chun and Madhani. 2010. Methods in Enzymology 470: 797 (PMID 20946836) has more information on how the knockout constructs were generated and how to propagate the strains.
2008 Madhani, set of 14 plates
(More information)
2015 Madhani plates (MS Excel)
The new 2015 set was received at the FGSC early in March 2015 and is available as complete set of 22 plates or individual clones.
Regarding the 2015 sets, the UCSF team has asked that we post the following statement about acknowledgement of the resource:
These knockout strains have been made freely available ahead of publication to the scientific community. It is requested that NIH funding (R01AI100272) for this project and the Madhani laboratory be acknowledged in any publication that uses this resource. Individuals interested in performing systematic, high-throughput analysis are asked to contact the Madhani lab to ensure coordination with ongoing efforts (hitenmadhani@gmail.com).
All of the 2015 deletion mutants are nourseothricin (NAT) resistant and can be propagated on YPD (or any other standard yeast media such as YNB or Sabouraud) supplemented with 0.1mg/ml NAT. We routinely use 0.075mg/ml NAT as we have found that specific activity of NAT varies from batch to batch. The parental strain KN99alpha is derived from H99 clinical isolate of C. neoformans Serotype A grubii and is a prototroph.
Chun and Madhani. 2010. Methods in Enzymology 470: p797 (PMID 20946836) has more information on how the knockout constructs are generated and how to propagate the strains.
In the figure, primer "1" corresponds to W1 in the spreadsheet , "2" to W2 etc.
For folks trying to determine what region is deleted at each locus, they can match the sequence of W2 and W5 (uppercase letters) to the genome. The sequence in between W2 and W5 has been replaced with the drug cassette. The lowercase letters of W2 and W5 primers are the sequences homologous to the drug cassette.
This database includes primer sequences
2016 Madhani plates (MS Excel)
The new 2016 set was received at the FGSC early in July 2016 and is available as complete set of 20 plates or individual clones.
2020 Madhani set of 7 plates (MS Excel)
Continuation of 2015 set of plates.
Available as a complete set of seven plates or as individual clones.
Received October 2020.
Deletion mutants are distributed as frozen cultures in 96- well plates or on agar solidified medium (additional fees apply).
We ask $100 per plate plus shipping. International destinations require special clearance and pre-approval.
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2/19/2021
