Fig. 1: RNA-seq analyses and validation of target genes ex vivo.
From: Identification of age-specific gene regulators of La Crosse virus neuroinvasion and pathogenesis
a Sequential approach to select target genes from RNA-seq analyses on vehicle (V) or Poly I:C (PI)-treated weanling (W) or adult (A) mice (WV, WPI, AV, and API). b Identification of target genes from RNA-seq analyses of microvessel fragments from olfactory bulb (OB) and cortex (CT) regions of weanling LACV infected (LOB and LCT) and mock inoculated mice (MOB and MCT) (N = 3 for all RNA-seq samples). The default DESeq function with betaPrior = FALSE was applied, wherein a negative binomial generalized model with Wald test for significance was performed. The two-sided p-values were corrected for multiple testing using the Benjamini Hochberg method. c–e Differential expression of representative genes, as validated by real-time PCR analyses on ex vivo isolated microvessel fragments from weanling mock (WM), weanling LACV (WL), adult mock (AM) and adult LACV (AL) infected mice. Gene categories: (c) intrinsic adult-specific (for Efna2 and H2q6 WM vs AM P = 0.0032 and P = 0.0001 and WL vs AL P = 0.0002 and P = 0.0356), d intrinsic weanling-specific (for Bst1 and Mmp25 WM vs AM P < 0.0001 and P = 0.1010 and WL vs AL P < 0.0001 and P = 0.4684) or (e) LACV-infection induced, adult enhanced genes (for Clec4e and Cldn1 WM vs AM P = 0.0453 and P = 0.0894 and WL vs AL 0.6490 and P = 0.5686). f Differential expression of representative genes from OB and CT microvessel fragments obtained from LACV-infected adults (AOB and ACT) and weanlings (WOB and WCT). P = 0.0043 and P = 0.0068 for Aqp1 and Ttr for WOB vs WCT comparison and P = 0.0417 and P < < 0.0001 for Aqp1 and Ttr for AOB vs ACT comparison. The data in (c–f) were transformed to log2 scale for a more normal distribution and the datapoints were statistically analyzed or plotted post-transformation. Significance values were measured by one-way ANOVA followed by Tukey’s multiple comparison (c–e) or two-tailed, multiple unpaired t-tests (f) (N = 5–6 for all mouse experiments, from Panel c–f and individual datapoints are shown). (*P < 0.05, **P < 0.01, ***P < 0.001 and ****P < 0.0001).
