Table of Kallisto quantification, limma statistics, and annotations for differentially expressed genes.

Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript with the UNIQID column giving the Broad Cp Silveira systematic gene name. The NAME column gives manually curated short gene names, transferred from Histoplasma capsulatum G217B (HcG217B, GenBank GCA_017607445.1) augmented with Coccidioides-specific gene names. The next three columns give limma BH-adjusted p-values for differential expression in each of the three contrasts. The next 8 columns give kallisto estimated counts for each sample. The next 8 columns give kallisto normalized abundances (TPMs) for each sample. Cp_GenBank and Cp_anno give the GenBank Cp Silveira accession and annotation respectively. CiRS, CiRS_GenBank, and Ci_anno give the Broad systematic gene name, GenBank accession, and annotation respectively for the InParanoid-mapped C. immitis RS ortholog. HcG217B, HcG217B_anno, and HcG217B_GenBank give the GSC systematic gene name and annotation (from [50]) and GenBank accession for the InParanoid-mapped HcG217B ortholog. Cp_new_GenBank gives the GenBank accession for the corresponding gene in the newly available Cp Silveira assembly and annotation (BioProject PRJNA664774) [51]. Class indicates the differential expression pattern, as referenced in the results and discussion sections. BGCOLOR gives the hex code for the class coloring in Fig 3. GWEIGHT is a place-holder column for JavaTreeView compatibility. The final three columns give the limma fit values for the three contrasts plotted in Fig 3.
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