Table 2 RNA-sequencing identified differential expression of transcripts related to the MAPK pathway and to cytokine-related processes, comparing gene expression in the ileum of little brown bats (Myotis lucifugus) infected only with the M. lucifugus coronavirus (Myl-CoV; virus-infected) or co-infected with Myl-CoV and Pseudogymnoascus destructans. The last 2 columns show the same comparisons made after grouping bats that were not exposed to the fungus, and bats that were exposed to the fungus and exhibiting symptoms of WNS (irrespective of their viral infection status).

Ensembl Gene Name	Ensembl Description	Virus-infected vs. Co-infected		All bats “without fungus” vs. all bats “with fungus”^a
Ensembl Gene Name	Ensembl Description	Log₂ Fold Change^b	Padj	Log₂ Fold Change^b	Padj
MAPK pathway-related transcripts
STYK1	serine/threonine/tyrosine kinase 1	−1.268	0.025	−1.516	<0.0001
RSU1	Ras suppressor protein 1	1.102	0.004
RRAD	RRAD, Ras related glycolysis inhibitor and calcium channel regulator	−1.297	0.028	−1.3	0.025
RERG	RAS like estrogen regulated growth inhibitor	1.562	0.018	1.416	0.005
MAP3K11	mitogen-activated protein kinase 11	−1.14	0.040	−1.13	0.0002
SRC	SRC proto-oncogene, non-receptor tyrosine kinase	−1.539	0.013	−1.297	0.0037
Cytokine-related transcripts
IRF1	Interferon regulatory factor 1	−1.551	0.001	−1.444	0.0001
IFI6	Interferon alpha inducible protein 6	−1.798	0.014	−1.352	0.039
IL22RA1	Interleukin 22 receptor subunit alpha 1	−1.411	0.015	−1.314	0.002
SOCS6	Suppressor of cytokine signaling 6	−1.278	0.008	−1.534	<0.0001

^a(Uninfected + virus-infected) vs. (fungus-infected + co-infected)
^bPositive log2 fold-change values indicate higher expression in the second listed treatments relative to the first.

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