mRNA-seq time course (in parallel to ATAC-seq time course), of wildtype C. elegans larvae sampled from 14h to 30h at 25oC [RNAseq_N2]
We collected timecourse samples for RNA-seq, in parallel to ATAC-seq, in order to have matching samples for comparisson. The overall goal was to link oscillating gene expression (RNA-seq) to oscillating changes in chromatin accessibility (ATAC-seq), in order to identify enhancer elements that are critical to oscillatory regulation. Overall design: mRNA-seq of RNA isolated from larval C. elegans (N2 strain) in a time course spanning 16 hours of development. Synchronized L1 animals were seeded (2000 animals per plate) on multiple 10 cm NG 2% plates coated with OP50 bacteria, and then 1 plate per timepoint (2000 animals) was harvested every hour starting 14 hours after seeding. RNA was isolated with Trizol and the Direct-zol RNA microprep kit (R2062, Zymo Research) including DNase treatment. Libraries were prepared according to the TruSeq Illumina mRNA-seq (stranded - high input) protocol. Library was sequenced using Hiseq 50 Cycle Single-end reads. In these experiments, samples were collected in parallel for mRNA-seq and ATAC-seq. And two independent experimental replicates were performed.