Differential Gene Expression and Pathway Analysis
The non-transformed transcript count matrix was input into DESeq2 (Love, Huber, & Anders, 2014) v.1.23.6 to determine differentially expressed transcripts among each lake-by-lake comparison at p ≤ 0.05 after Benjamini-Hochberg false discovery rate (FDR) correction. Differentially-expressed transcripts that were annotated were input into ToppGene Suite (Kaimal, Bardes, Tabar, Jegga, & Aronow, 2009) to identify altered KEGG pathways and GO terms among lakes.