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. 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)..我们对10~12周龄雄性C57BL/6J小鼠的大脑皮层开展了基因表达与染色质可及性监测，监测周期覆盖单次全睡眠剥夺（total sleep deprivation, SD）结束前24小时至结束后48小时，旨在解析全睡眠剥夺后的机体响应及后续恢复过程。小鼠于明暗周期的光照起始时刻（ZT0-ZT6，对应时间区间24~30）开始接受6小时的全睡眠剥夺。对照组（非睡眠剥夺组，Non Sleep Deprived, NSD）于实验首日的ZT0、ZT3、ZT6、ZT12、ZT18时刻实施安乐死，对应样本编号为T0-T24，覆盖全睡眠剥夺前的24小时，以此作为基线日（第0日）的对照样本。第1日，全睡眠剥夺组小鼠在与第0日相同的时刻被安乐死，对应样本编号为T27-42，其中T27、T30样本分别采集于睡眠剥夺3小时、6小时后；第2日采样时刻为ZT0、ZT6、ZT12、ZT18，对应样本编号T48-66；第3日采样时刻为ZT0、ZT6，对应样本编号T72-78。另有两组小鼠在全睡眠剥夺后恢复7天，于第8日的ZT0、ZT6时刻安乐死，对应样本编号T192-198。每个时间点与处理条件设置3~4次生物学重复，同时采集了来自2批不同实验动物的ZT0对照组样本，共计8次重复。RNA测序（RNAseq）与转座酶可及性测序（ATAC-seq）文库均取自同一只小鼠，即本数据集为配对数据集。T66时间点的2个ATAC-seq文库测序失败，仅剩余1次生物学重复（对应该时间点的RNAseq未受影响，仍保留3次生物学重复）。