| Antibodies |
| Monoclonal ANTI-FLAG® M2 antibody |
Sigma-Aldrich |
Cat# F3165; RRID: AB_259529 |
| IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody |
LI-COR Biosciences |
Cat# 926-68070; RRID: AB_10956588 |
| Bacterial and virus strains |
|
Cryptococcus neoformans: KN99a and KN99α (38) |
Joe Heitman, Duke University |
[] |
|
Cryptococcus neoformans: clinical and environmental isolates |
John Perfect, Duke University |
This paper, Supplemental Table 1A
|
|
Cryptococcus neoformans: clinical isolates |
CINCH Consortium |
This paper, Supplemental Table 1A
|
|
Cryptococcus neoformans: gene deletion library (4) |
Fungal Genetics Stock Center |
Madhani plates (2015, 2016, 2020) |
|
Cryptococus neoformans: engineered strains |
Authors |
This paper, Supplemental Table 1B and 1D
|
|
Cryptococcus neoformans: recombinant strains |
Authors |
This paper, Supplemental Table 1B
|
| Chemicals, peptides, and recombinant proteins |
| Yeast extract |
Fisher Scientific |
Cat# DF0127179 |
| Bacto peptone |
ThermoFisher |
Cat# 211677 |
| Phosphate buffered saline |
Fisher Scientific |
Cat# MT21040CM |
| V8 juice |
Campbell Soup Company |
|
| RPMI medium |
Sigma-Aldrich |
Cat# R8758-6X500ML |
| Mouse serum |
BioIVT |
Cat# MSE01SRMUN5, lot # MSE308112 |
|
13C-5-adenosine cAMP |
Toronto Research Chemicals |
Cat # A280457 |
| Critical commercial assays |
| TRIzol reagent |
Ambion |
Cat# 15-596-018 |
| NEBNext Ultra RNA Library Prep Kit for Illumina |
New England Biolabs |
Cat# E7420L |
| NEBNext Poly(A) mRNA Magnetic Isolation Module |
New England Biolabs |
Cat# E7490L |
| NEBNext Ultra II DNA Library Prep Kit for Illumina |
New England Biolabs |
Cat# E7645L |
| Deposited data |
| Whole genome sequence data |
Sequence Read Archive project number PRJNA967729 |
Accession numbers listed in Supplementary Table 1A–D
|
| RNA-seq data |
Gene Expression Omnibus (GEO) project number GSE232437
|
Accession numbers listed in Supplementary Table 1E
|
| Proteomics data |
PRIDE: Proteome Xchange |
Accession number: PXD045163 |
| Experimental models: Organisms/strains |
| Mice: C57Bl/6 |
Jackson Laboratory |
Cat#000664 RRID:IMSR_JAX:000664 |
| Software and algorithms |
| GraphPad Prism 9 |
GraphPad Software, Inc. |
|
| NextGenMap |
Sedlazeck et al. (64) |
https://cibiv.github.io/NextGenMap/
|
| SAMtools |
Li et al. (65) |
http://www.htslib.org/
|
| Lumpy |
Layer et al. (66) |
https://github.com/arq(5)x/lumpy-sv
|
| Yaha |
Faust et al. (67) |
https://github.com/GregoryFaust/yaha
|
| MergeSamFiles from Picard tools version 2.10.0 |
Broad Institute |
https://github.com/broadinstitute/picard
|
| FreeBayes version 1.1.0 |
Garrison et al. (68) |
https://github.com/freebayes/freebayes
|
| SNPEff version 4.3.1 |
Cingolani et al. (69) |
https://pcingola.github.io/SnpEff/
|
| CNVnator 0.3.2 |
Abyzov et al. (70) |
https://github.com/abyzovlab/CNVnator
|
| QTLseqr |
Mansfield et al. (71) |
https://github.com/bmansfeld/QTLseqr
|
| FastQC |
Wingett et al. (75) |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| Hisat2 version 2.2.1 |
Kim et al. (76) |
http://daehwankimlab.github.io/hisat2/
|
| Subread 2.0.0 |
Liao et al. (77) |
https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html
|
| DESeq2 |
Love et al. (78) |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Bulk Segregant Analysis (BSA) and Association Analysis (AA) |
This paper |
https://github.com/DanielPAagustinho/BSA_crypto_analysis
|
| IHW (independent hypothesis weighting) package |
Ignatiadis et al. (79) |
https://github.com/nignatiadis/IHW
|
| MaxQuant software (version 2.0.3) |
Cox et al. (82) |
https://maxquant.net
|
