Figure 3

Transcriptome analysis. Gene expression profiles were evaluated by RNAseq for all LND (n = 6) and control (n = 6) lines. Differential gene expression differed according to both analytical method (edgeR, DESeq2) and statistical threshold (A). However, 403 genes were differentially expressed using both methods at FDR < 0.05 (B). For both edgeR and DESeq2 methods, volcano plots (C) consistently demonstrate 2 genes to be expressed at markedly lower levels in the LND lines (HPRT1 and FAR2P1), and 1 gene to be expressed at higher levels in the LND lines (RNF39). The red color shows genes with FDR < 0.05 and fold change > 2. The blue color shows genes with FDR < 0.05 and fold change < 2. Green and gray show gene changes with FDR > 0.05. Individual variation among the lines is shown as a heatmap of gene expression (D). Red depicts higher gene expression and green depicts lower expression. Considering only the 403 genes differentially expressed using both edgeR and DESeq2 at FDR < 0.05, 19 pathways appeared to be significantly different when comparing the LND and control lines (E). Red bars depict positive z-scores while green depict negative z-scores. Red dots represent p-values < 0.001 (i.e. − log10(.001) > 3.