This repository is supplementary data accompanying the bioRxiv preprint:

A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201. Elizabeth S. Hughes, Zhenzhen He, Laura R. Tuck, Elizabeth R. Ballou, Edward W.J. Wallace. bioRxiv preprint, 2023 https://doi.org/10.1101/2023.06.14.543486

Data Analysis by Edward Wallace [email protected] and Liz Hughes [email protected].

This repository holds most supplementary data and analysis for the paper:

• budding index analysis
• colony-forming unit assays
• growth curve assays by plate reader
• RT-qPCR

RNA-seq data analysis and homology analysis are in separate repositories:

• RNA-seq dataset 1 https://github.com/ewallace/CryptoWakeupRNASeq
• RNA-seq dataset 2 https://github.com/ewallace/CryptoGat201RNASeq
• Homology https://github.com/ewallace/Gat201homology_2022/

Contents of the repository, listed by directory.

Data analysis scripts, in R markdown .Rmd format. Also the .html format output.

• budding_index.Rmd - makes Figure 2B
• colony_forming_units_RPMI_RPMIserum.Rmd - makes Figure 2D
• growth_curves_GAT201_RPMI_YPD.Rmd - makes Figure 2C
• growth_curves_GAT201targets.Rmd - makes Figure 4E, Figure S10
• growth_curves_GAT204_LIV3.Rmd - makes Figure S11
• growth_curves_GAT201_RPMIvCO2Indep.Rmd - makes Figure S12
• growth_curves_GAT201_RPMI_varyingNaHCO3.Rmd - makes Figure 5, Figure S13
• growth_curves_GAT201_RPMI_NaHCO3_vs_cAMP.Rmd - makes Figure S14
• RTqPCR_GAT201_complemented_strains.Rmd - makes Figure S6
• shared_functions_formatting.Rmd - shared packages, functions, and figure formatting that is called in all other data analysis scripts.

Input data files in various tabular formats (.xlsx, .csv, .txt).

Contents here listed by the .Rmd analysis script that uses them.

• 20220811_CryptoWakeup_Gat201_budding_quantification.xlsx

• 20221025_CFU60_RPMI_RPMIserum.csv

• 20200728_EH_PR2_RPMI_Setup.csv
• 20200728_EH_PR2_RPMI_WT_Gat201.xlsx
• 20200807_EH_PR4_YPD_Setup.csv
• 20200807_EH_PR4_YPD_WT_Gat201.xlsx

• 20230308_RPMI_Gat201Targets_Plate1_setup.csv
• 20230308_RPMI_Gat201Targets_Plate1.xlsx
• 20230310_RPMI_Gat201Targets_Plate2_setup.csv
• 20230310_RPMI_Gat201Targets_Plate2.xlsx
• 20230321_RPMI_Gat201Targets_Plate3_setup.csv
• 20230321_RPMI_Gat201Targets_Plate3.xlsx

• 20240403_GAT204LIV3.xlsx
• 20240403_GAT204LIV3_Setup.csv

• 20221216_PR27_RPMIvCO2Indep_Setup.csv
• 20221216_PR27_RPMIvCO2Indep.xlsx

• 20240112_SubGoal4_BR1_repeat.xlsx
• 20240112_SubGoal4_BR2_repeat.xlsx
• 20240112_SG4_BR3.xlsx
• 20240116_SG4_Plate-Setup.csv

• 20240305_cAMP_Assay.xlsx
• 20240305_cAMP_Plate_Setup.csv

• 20221014_ComplementCheck_EH_Ct.txt

Results files, mostly figures.

Contents here listed by the .Rmd analysis script that produces them.

• budding_index_Time_Media_Temp.png
• budding_index_Time_Media_Temp.svg

• cfu_mean_plot_all_RRS.png
• cfu_mean_plot_all_RRS.svg

• 20200728_EH_PR2_RPMI_WT_Gat201_summaryplot.png
• 20200807_EH_PR4_YPD_WT_Gat201_summaryplot.png
• fig_growthcurves_GAT201_RPMI_YPD.svg
• fig_growthcurves_GAT201_RPMI_YPD.png

• fig_growthcurves_Gat201Targets_RPMI_summary.png
• 20230308_RPMI_Gat201Targets_Plate1_splineplot.png
• 20230308_RPMI_Gat201Targets_Plate1_splineplot.svg

• fig_growthcurves_GAT204_LIV3.png

• fig_growthcurves_RPMI_CO2independent.png

• fig_growthcurves_varyingNaHCO3_BioRep3.png
• fig_growthcurves_varyingNaHCO3_allreps.png

• fig_growthcurves_NaHCO3_vs_cAMP.png

• RTqPCR_GAT201_complemented_strains_deltadeltacq.png