ATAC-seq time course (in parallel to mRNA-seq time course), of wildtype C. elegans larvae sampled from 14h to 30h at 25oC [ATACseq_N2]
We collected timecourse samples for ATAC-seq, in parallel to mRNA-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: ATAC-seq was performed on nuclei 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 7 plates per timepoint (14000 animals) were harvested every hour starting 14 hours after seeding. Nuclei were prepared from frozen animal pellets by douncing similar to a previosuly established protocol (Daugherty et al., 2017, Genome Res.). Library was sequenced using the NextSeq HIGH-OUT 75 Cycle Paired-end protocol. In these experiments, samples were collected in parallel for mRNA-seq and ATAC-seq. And two independent experimental replicates were performed.