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