mRNA-seq time course of C. elegans sampled at and after release from dauer starvation at 25 degrees

We find that the 'high-confidence oscillating' genes initiate oscillations similarly as after release from L1 dauer. We performed high-throughput RNA sequencing on worms that were synchronously released from the dauer stage by refeeding on OP50. In particular, we investigate oscillatory gene expression as described in Hendriks et al., 2014 (doi: 10.1016/j.molcel.2013.12.013) and observe the re-initiation of oscillatory gene expression from stable expression with a time delay upon dauer exit. Experimental observation of the transitions between non-oscillatory and oscillatory states during the first 5 hours after dauer exit reveals that the oscillatory gene expression is arrested in a specific oscillator phase, similar to the observation we make in animals released from L1 arrest (see Meeuse et al., 2020, doi: https://doi.org/10.1101/755421). Examination of gene expression profiles over time at 25 degrees, using high throughput mRNA sequencing. The "RNAseq_N2_dauer" sample was combined with the samples GSM1277134 - GSM1277155 (in GSE52861) and all samples were mapped to C. elegans genome (ce10) using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R followed by counting the reads using qCount() from the QuasR package in R. A pseudocount of 8 was added and then the counts were log2-transformed. For the pairwise correlation analysis described in XX we used the mean normalized gene expression of the "oscillating" gene set using pearson correlation.