2.5. RNA-seq
For transcriptomic analysis, RNA-seq was performed as described previously (Kim et al., 2015). Briefly, RNA was extracted from exponentially growing 0.5 mg cells of the control strain (SR7) and gcr2 mutant (SR7 gcr2 ) on glucose or xylose using a Qiagen RNeasy Mini Kit, and the RNA quality was evaluated using a Bioanalyzer RNA chip. The samples with high-quality total RNA were sequenced using an Illumina HiSeq 2000 system. The sequencing results were then analyzed using the CLC Genomic Workbench (version 6.5) to investigate RNA-seq quality, differentially expressed (DE) genes, and Gene Set Enrichment Analysis (GSEA). Fold changes were calculated based off the total number of exon reads per kilobase of exon length per million mapped reads (RPKM) between SR7 and SR7 gcr2 strains.
Results