Time course analysis of gene expression during hypoxia in several S. cerevisiae mutant strains using RNA-Seq

We used RNA-seq to monitor mRNA levels of all genes in response to hypoxia in several mutant strains of the yeast, S. cerevisiae (S288C background with wildtype HAP1). To gain insights into how gene expression changes over time, cells were subjected to 100% nitrogen gas and collected after 0,5,10,30,60,120,180, and 240 minutes. Total RNA was extracted and mRNAs were enriched by polyA selection. The cDNA was prepared into a sequencing library, multiplexed and single-end sequenced by an Illumina HiSeq 2500 sequencer. After mapping with Tophat2, the number of reads per feature was calculated using HTSeq. RNA-seq analysis of eight time points of a yeast strain grown in hypoxia. The time course course is repeated in different mutant strains.