Sleep-wake driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

We monitored gene expression and chromatin accessibility in the cerebral cortex of 10-12 week-old male C57BL/6J mice for 24 hours before and until 48 hours after the end of a single total sleep deprivation (SD) episode. The aim was to characterise the response to SD and recovery thereafter. Overall design: Mice were sleep deprived for 6 hours starting at light onset (ZT0-ZT6; Time 24-30) of the light-dark cycle. Control mice (NSD, Non Sleep Deprived) were sacrificed at ZT0, ZT3, ZT6, ZT12, ZT18 of the first day of experimentation (named samples T0-T24 and corresponding to the 24 hours before SD), serving as a baseline day (Day 0). On Day 1, SD mice were sacrificed at the same time of day as on Day 0 (samples T27-42, with T27 and T30 samples being taken after 3h and 6h SD, respectively), on Day 2 at ZT0, ZT6, ZT12, ZT18 (samples T48-66), as well as ZT0 and ZT6 on Day 3 (samples T72-78). Two groups of mice were allowed to recover for 7 days after SD, before being sacrificed at ZT0 and ZT6 (Day 8, samples T192-198). We collected 3-4 replicates per time point and condition, and 8 replicates of ZT0 controls from two different animal batches. RNAseq and ATAC-seq libraries originate each time from the same animal, i.e. the data sets are paired. Sequencing failed for 2 ATAC-seq libraries at T66, resulting in only one biological replicate at this time point (corresponding RNAseq was not affected and thus comprises 3 biological replicates)..