Abstract
We have generated detailed RNA-seq data for the nematode C. elegans with high temporal resolution in the embryo as well as representative samples from postembryonic stages across life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period where histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We have annotated internal promoter usage in operons using SL1 and SL2 data. We have also uncovered correlated transcriptional programs that span more than 80kb. These data provide detailed annotation of the C. elegans transcriptome.