title: RNAseq of Trichophyton rubrum
design: T. rubrum ACTC 28188 (1  106 conidia/mL) was inoculated into 100 mL of RPMI-GM (pH 5.0) and incubated at 30C for 96 hrs with agitation. Mycelium was then harvested by filtration and transferred to RPMI-GM (pH 5.0) with or without 0.1 mM NaHS, followed by incubation at 30C for 3 hrs under agitation. The samples were subsequently stored at 80C until RNA extraction. Total RNA was extracted from frozen mycelia (approximately 100 mg) using the Illustra RNAspin Mini RNA Isolation Kit (GE Healthcare, Chicago, IL, USA) following the manufacturers instructions. After extraction, the RNA quantity and integrity were assessed using the Qubit RNA BR Assay Kit and the Qubit RNA IQ Assay Kit, respectively, with a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Paired-end 100bp sequencing was performed by BGI Tech Solutions (Warszawa, Poland) using a DBN sequencer following the construction of an rRNA depletion library. For each of the conditions (with or without 0.1 mM NaHS), 4 independent samples were sequenced. FastQ sequencing files were analysed using Fastqc and produced a quality score of > 36. Raw sequencing files were splice-aligned to the T. rubrum CBS118892 reference genome (ASM151142v1 in NCBI (GCF_000955945.1 Refseq)) using Hisat2 [72], producing a mean % alignment of 54.4%. Differential expression analysis was undertaken with DESeq2, using the NCBI ASM151142v1 reference database. P values were adjusted for transcriptome-wide false discovery rate (FDR), with an adjusted significance threshold of q < 0.05.  Genes were classified based on Gene Ontology (GO) annotation derived from Uniprot ( niport.org), and GO enrichment analysis was performed using the FungiDB platform, using an adjusted (Benjamini) p value of < 0.05).