RNA-seq analysis of Saccharomyces cerevisiae and Ogataea parapolymorpha in heat shock response to find out if the response was homologous in two organisms, despite they differ in growth temperature. R or Rmd combined with existing bioinformatics tools will be used for analysis.
First, experimental design of heat shock response in two species, BY4741 for Saccharomyces cerevisiae and DL-1 for Ogataea parapolymorpha. Library for each biological sample with replicates is created for RNA sequencing. Single-end or both-ends of RNA are sequenced to generate millions of reads. The read sequence and quality information is output into FASTQ files, where the quality of raw data is assessed by FastQC, preventing contamination by adaptors by Cutadapt. These reads are then mapped to reference genome. Following mapping, reads aligned to exons of each gene are quantified in counting matrix, indicating level of gene expression. Differential expression analysis is then performed by DESeq2. To extract biological meaning of RNA-seq data, gene ontology analysis will be applied to classify genes into different function groups. Finally, expression profile in heat shock condition of different yeast strains are compared.