KEY RESOURCES TABLE.
| Reagent or resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Purified anti-mouse CD16/32 antibody (93) | BioLegend | Cat#101302; RRID:AB_312800 |
| PE anti-mouse F4/80 antibody (BM8) | BioLegend | Cat#123110; RRID:AB_893498 |
| APC/Cy7 anti-mouse/human CD11b antibody (M1/70) | BioLegend | Cat#101226; RRID:AB_830642 |
| Pacific Blue anti-mouse Ly-6C antibody (HK1.4) | BioLegend | Cat#128014; RRID:AB_1732079 |
| PE anti-mouse CD45 antibody (30-F11) | BioLegend | Cat#103105; RRID:AB_312970 |
| FITC anti-mouse Ly-6G antibody (1A8) | BioLegend | Cat#127606; RRID:AB_1236494 |
| Fc(human):Dectin-1 antibody | AdiopenGen | Cat#AG-40B-0138-C050 |
| Alexa Fluor® 488 anti-human IgG Fc (HP6017) | BioLegend | Cat#409322; RRID:AB_2563437 |
| Rabbit anti-phospho-p40phox (Thr154) antibody | Cell Signaling | Cat#4311; RRID: AB_330690 |
| Mouse anti-panERK antibody | BD Biosciences | Cat#610123; RRID:AB_397529 |
| Rat anti-HA antibody, HRP | Roche | Cat#12013819001; RRID:AB_390917 |
| Goat anti-mouse IgG (H+L) secondary antibody, HRP | Thermo Fisher Scientific | Cat#31430; RRID:AB_228307 |
| Mouse anti-β-actin (D6A8) antibody | Abcam | Cat#8224; RRID:AB_449644 |
| Goat anti-rabbit IgG (H+L) secondary antibody, IRDye 800CW | LI-COR | Cat#926–32214; RRID:AB_621846 |
| Goat anti-mouse IgG (H+L) secondary antibody, IRDye 800CW | LI-COR | Cat#926–32210; RRID:AB_621842 |
| Goat anti-rabbit IgG (H+L) secondary antibody, HRP | Cell Signaling | Cat#7074; RRID:AB_2099233 |
| Rabbit anti-Sap2 polyclonal antibody | Kuchler Laboratory | N/A |
|
Chemicals, peptides, and recombinant proteins | ||
| Yeast extract | BD Biosciences | Cat#212720 |
| Peptone | BD Biosciences | Cat#211820 |
| Dulbecco’s Phosphate Buffered Saline | Sigma-Aldrich | Cat#D8537 |
| DMEM | Thermo Fisher Scientific | Cat#11584486 |
| RPMI-1640 | Thermo Fisher Scientific | Cat#21875 |
| Fetal calf serum | Sigma-Aldrich | Cat#F7524 |
| Bovine serum albumin | Sigma-Aldrich | Cat#A2153 |
| Yeast carbon base | Sigma-Aldrich | Cat#Y3627 |
| Yeast nitrogen base withoug ammonium sulfate and aa | BD Biosciences | Cat#233520 |
| Pepstatin A | Sigma-Aldrich | Cat#516481 |
| Zymosan A | Sigma-Aldrich | Cat#Z4250 |
| Trehalose-6,6-dibehenate (TDB) | InvivoGen | Cat#INV-tlrl-tdb |
| RNA/ater™ Stabilization Solution | Thermo Fisher Scientific | Cat#AM7022 |
| Nextera TDE1 | Illumina | Cat#15027865 |
| Complete, EDTA-free Protease Inhibitor Cocktail Tablets | Roche | Cat#04693132001 |
| Zombie Aqua Fixable Viability Dye | BioLegend | Cat#423101 |
| Fixation buffer | BioLegend | Cat#420801 |
|
Critical commercial assays | ||
| MinElute PCR purification kit | QIAGEN | Cat#28006 |
| RNeasy MinElute Cleanup kit | QIAGEN | Cat#74204 |
|
Deposited data | ||
| RNA-seq raw data | This study | GEO: GSE157411 |
| ATAC-seq raw data | This study | GEO: GSE157411 |
| Mass-spectrometry data from SC medium culture supernatants | This study | PRIDE: PXD018163 |
|
Experimental models: Primary cells | ||
| Murine bone marrow derived macrophages | This study | N/A |
| Murine bone marrow derived neutrophils | This study | N/A |
|
Experimental models: Organisms/strains | ||
| C57BL/6J mice | Jackson Laboratory | Cat#000664; RRID:IMSR_JAX:000664 |
| C. albicans: wild type (WT) | (Gillum et al., 1984) | N/A |
| C. albicans: Clinical isolate 1 | Birgit Willinger | AKH No. 2284 |
| C. albicans: Clinical isolate 10 | Birgit Willinger | AKH No. 2275 |
| C. albicans: hir1Δ/Δ | (Tscherner et al., 2015) | CASJ019 |
| C. albicans: hir1 Δ/Δ::HIR1 | (Jenull et al., 2017) | CASJ013 |
| C. albicans: Clinical isolate 1 hir1Δ/Δ | This study | CASJ255 |
| C. albicans: Clinical isolate 10 hir1 Δ/Δ | This study | CASJ252 |
| C. albicans: hat1 Δ/Δ | (Tscherner et al., 2015) | CA-MT014 |
| C. albicans: cac2Δ/Δ | (Tscherner et al., 2015) | CA-MT363 |
| C. albicans: sap2Δ/Δ | (Staib et al., 2008) | SAP2MS4A |
| C. albicans: sap2Δ/Δ hir1 Δ/Δ | This study | CASJ261 |
| C. albicans: sap3Δ/Δ | This study | CASJ301 |
| C. albicans: hir1 Δ/Δ sap3Δ/Δ | This study | CASJ304 |
| C. albicans: sap2Δ/Δ sap3Δ/Δ | This study | CASJ308 |
| C. albicans: sap2Δ/Δ sap3Δ/Δ hir1 Δ/Δ | This study | CASJ310 |
| C. albicans: stpl Δ/Δ | This study | CASJ403 |
| C. albicans: hir1 Δ/Δ stp1Δ/Δ | This study | CASJ405 |
| C. albicans: ssy5Δ/Δ | (Miramon and Lorenz, 2016) | CaPM23 |
| C. albicans: ssy5Δ/Δ hir1 Δ/Δ | This study | CASJ420 |
| C. albicans: pmr1 Δ/Δ | This study | CASJ224 |
| C. albicans: hir1 Δ/Δ pmr1 Δ/Δ | This study | CASJ226 |
| C. albicans: pmr1 Δ/Δ::PMR1 | This study | CASJ239 |
| C. albicans: hir1 Δ/Δ pmr1Δ/Δ::PMR1 | This study | CASJ241 |
| C. albicans: chs3Δ/Δ | This study | CA-MT611 |
| C. albicans: chs3Δ/Δ hir1Δ/Δ | This study | CASJ262 |
|
Oligonucleotides | ||
| See Table S1 for full oligonucleotide list | N/A | |
|
Recombinant DNA | ||
| Plasmid: pSFS3b | (Tscherner et al., 2012) | N/A |
| Plasmid: YEp352 | (Hill et al., 1986) | N/A |
| Plasmid: pFA6a-3xHA-SAT1-FLP | This study | pFA6a-3HA-SAT 1-FLP |
| Plasmid: YEp-SAP3urdr-FLP-NAT1 | This study | ECSJ071 |
| Plasmid: YEp-PMR1urdr-FLP-NAT1 | This study | ECSJ031 |
| Plasmid: YEp-PMR1 reint-FLP-NATI | This study | ECSJ082 |
| Plasmid: YEp-CHS3urdr-FLP-NAT1 | This study | YEp352-NAT1-CHS3urdr |
| Plasmid: Yep-STP1urdr-FLP-NAT1 | This study | ECSJ075 |
|
Software and algorithms | ||
| fastQC v v0.11.8 | (Andrews, 2010) | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| cutadapt v1.18 | https://cutadapt.readthedocs.io/en/stable/ | |
| NextGenMap v0.5.5 | (Sedlazeck et al., 2013) | https://cibiv.github.io/NextGenMap/ |
| Picard | Broad Institute | http://broadinstitute.github.io/picard/ |
| BEDTools | https://github.com/arq5x/bedtools2 | |
| HTseq | (Anders et al., 2015) | https://htseq.readthedocs.io/en/master/ |
| edgeR | (Robinson et al., 2010) | https://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
| MACS2 v2.1.2 | (Zhang et al., 2008) | https://github.com/macs3-project/MACS |
| ChIPseeker | (Yu et al., 2015) | http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| deepTools2 | (Ramírez et al., 2016) | https://deeptools.readthedocs.io/en/develop/ |
| clusterProfiler | (Yu et al., 2012) | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| MaxQuant v1.6.2.6 | (Cox and Mann, 2008) | http://www.maxquant.org/ |
| ProteinPilot v5.0.1 | SCIEX | https://sciex.com/products/software/proteinpilot-software |
| Peakview v2.2 | SCIEX | https://sciex.com/products/software/peakview-software |
| MSStats | (Choi et al., 2014) | https://www.bioconductor.org/packages/release/bioc/html/MSstats.html |
| R v3.6.1 | R Core Team 2019 | https://www.R-project.org/ |
| RStudio v1.3.1093 | RStudio Team 2020 | https://www.rstudio.com/ |
| FlowJo software version 7.6.5 and 10.7.1 | FlowJo | N/A |
| Realplex software 2.0 | Eppendorf | N/A |
| GraphPad Prism version 6.0 | GraphPad | N/A |
| RNA-seq analysis script | This study | https://github.com/tschemic/RNAseq_analysis |
| ATAC-seq analysis script | (Jenull et al., 2020) | https://github.com/tschemic/ATACseq_analysis |
|
Deposited raw data | ||
| RNA-seq raw data | This study | GSE157411 (GSE157599 SuperSeries) |
| ATAC-seq raw data | This study | GSE157568 (GSE157599 SuperSeries) |
| Mass spectrometry raw data (SC culture supernatants) | This study | PXD018163 |
|
Other | ||
| RNA 6000 Nano Kit | Agilent | Cat#5067–1511 |
| High Sensitivity DNA Kit | Agilent | Cat# 5067–4626 |