Differential expression analysis of Lactiplantibacillus plantarum transcriptome during growth in EET-conducive conditions

DESeq2 analysis of L. plantarum transcriptome data using the Wald test in the R-studio shiny app DEBrowser (ver 1.14.2) was used to quantify differential gene expression based on culture conditions stimulating extracellular electron transfer (EET) (methods described here: https://doi.org/10.1101/2021.05.26.445846). The significance cutoff for differential expression was set to a False-discovery-rate (FDR)-adjusted p-value < 0.05 and a Log2 (fold-change) > 0.5. Clusters of Orthologous Groups (COGs) were also assigned to genes based the eggNOG (ver. 5.0) database. L. plantarum raw RNA-seq data are available in the NCBI Sequence Read Archive (SRA) under BioProject accession no. PRJNA717240.