RNA-Seq Analysis of Wild Type and Scn5aΔ/+ left ventricle at dark:light and light:dark phase transitions

We investigated differences in gene expression in left ventricular tissue from WT and ΔKPQ (Scn5aΔ/+) mice. Tissue was collected diurnally at the phase transitions from dark to light (D:L) and light to dark (L:D). We employed RNAseq (Novogene) to examine potential variances between the two strains of mice, as well as, any differences in expression at the two time points. RNAseq provided a snapshot of gene expression which revealed an intact molecular clock for both strains. Previous studies have demonstrated circadian peak or trough at the light phase changes in cardiac tissue in mice for many core molecular clock components. Similar to these studies both strains demonstrated a significant difference in expression between core molecular clock genes Bmal1, Clock, Per1, Per2, Per3 assessed at the phase transitions. This assessment revealed 39 diurnally expressed genes. To our surprise, only 6 genes were differently expressed between the two strains of mice. Ventricular mRNA profiles of wild type (WT) and ΔKPQ (Scn5aΔ/+) mice 12 months of age were generated by deep sequencing, 3 pooled samples for each strain/timepoint, using Novogene RNA-seq, Illumina Platform PE150 (NovoSeq 6000)