Studies of bacterial-fungal spatial interaction
The reads were aligned to each reference genome (S. aureus USA300 reference; GCF_ 000013465.1_ASM1346v1, M. restricta reference; GCF_003290485.1_ASM329048v1) using Bowtie2 (version 2.3.4.1) and HISAT2 (version 2.1.0) alignment software [12]. Raw read counts were generated using HTseq (version 0.10.0)[1] and StringTie (version 2.1.3b) for each annotated gene. Differentially expressed gene (DEG) analysis was performed using EdgeR for comparative combinations (axenic- and co-cultured samples).