Bioinformatics analysis

RNA sequencing data from Herdy et al. (2019): libraries were prepared with TruSeq stranded mRNA sample prep kit (Illumina) and sequenced single-end 50 bp on Illumina HiSeq 2500 platform. Read trimming and mapping were performed using TrimGalore and STAR, respectively. Raw counts were generated using HTseq variance stabilizing transformation normalization (vst) and differential expression analysis was performed in DEseq2 with default Wald test for hypothesis testing. Cutoff for highly significant DEGs for this study was log2-fold change with a corresponding padj <0.01 (Herdy et al., 2019). Bioinformatics and statistics analyses of RNA-Seq data from Herdy et al. (2019) were performed with R version 4.1.1 and applied methods are indicated in figure legends. GSEA to compare gene expression changes (log2FC) between FBs and D20 iN in KEGG pathways was performed with R package clusterProfiler.