Fig. 2: Differential transcript expression and protein levels in SFTSV-infected R. microplus BME6 cells.

RNA and protein samples were prepared from mock or SFTSV-infected (MOI 1 PFU/cell) BME6 cells and analyzed for mRNA expression and protein biosynthesis in response to infection. a, b Differential RNA expression volcano plots. X axis represents the Log₂ Fold Change (Log₂FC) when comparing 3 d.p.i (a) or 6 d.p.i (b) to mock-infected cells. The y axis shows −Log₁₀(padj). Blue dots represent up-regulated transcripts, (Log₂FC ≥ 1.5, padj ≤ 0.05) and red dots down-regulated transcripts (log2FC ≤ −1.5, padj ≤ 0.05). Gray dots represent non-significantly regulated RNAs (padj ≥ 0.05). Differential gene expression analysis was performed using DESeq2, which models count data from RNA-seq experiments using negative binomial generalized linear models. Genes with an adjusted p value (Benjamini-Hochberg correction) below 0.05 were considered significantly differentially expressed. c Venn-diagram representing transcripts significantly differentially regulated (log₂FC ± 1.5, padj ≤ 0.05) at 3 or 6 d.p.i., blue and red diagrams represent up and down-regulation, respectively. d, e Differential protein abundance volcano plot. X axis represents the Log₂ Difference (Log₂D) when comparing 3 d.p.i. (d) or 6 d.p.i. (e) to mock infected cells. The y axis shows non-zero confidence for each protein (−log₁₀(p)). Significantly up-regulated proteins (blue dots) and down-regulated proteins (red dots) were identified using a modified t test (Perseus “one-sample, two-tailed t test” with s₀ = 0.02 and Benjamini–Hochberg FDR ≤ 0.05). Gray dots represent non-significantly regulated proteins. f Venn–diagram representing proteins significantly differentially regulated (Log₂FC ± 1.5, padj ≤ 0.05) at 3 and 6 d.p.i., blue and red diagrams represent up- and down-regulation, respectively. g, h Scatter plot showing the correlation between protein (Y axis) and mRNA (X axis) expression ratios, Log₂D and Log₂FC, respectively. Purple dots represent genes and/or proteins with padj ≤ 0.5. Density clusters, as defined by R software are represented by yellow lines. g Scatter plot showing differential expression of transcripts and proteins at 3 d.p.i. Pearson’s product-moment correlation analysis revealed a moderate positive correlation (r = 0.3). A two-tailed t test was used to assess whether the correlation differed significantly from zero (t = 7.1824, df = 534, p = 2.313 × 10⁻¹²). h Scatter plot for differential expression of transcripts and proteins at 6 d.p.i. Pearson’s product-moment correlation analysis revealed a moderate positive correlation (r = 0.13). A two-tailed t test was used to assess whether the correlation differed significantly from zero(t = 9.0447, df = 4370, p value < 2.2e-16). Source data are provided as Source Data file.