Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the murine cortex

Sleep loss regulates gene expression throughout the brain and impacts learning and memory. However, the molecular consequences of sleep deprivation and the ability of subsequent sleep (recovery sleep) to restore baseline gene expression remain underexplored. Our goal here is to overview transcriptional changes at the gene level in the cortex of adult male wildtype mice in response to sleep loss and recovery sleep. This dataset constitutes an integration of novel data with two publicly available RNA-seq studies and contains 3, 5, and 6 hours of sleep deprivation and 2 and 6 hours of recovery sleep time points. Overall design: We analyzed gene expression for 42 RNA-seq samples. Prefrontal cortex tissue was collected after 5 hours of sleep deprivation and 2 hours of subsequent recovery sleep, while cerebral cortex tissue was collected after 3 and 6 hours of sleep deprivation and 6 hours of subsequent recovery sleep. Animals that were left to sleep in their home cage were dissected at the same time of day as the animals in the corresponding treatment group to control for variations due to circadian rhythms. Our dataset is an integration of samples from GSE140345 and GSE113754 with unpublished and not previously analyzed data from our group that was collected at the same time as the samples from GSE113754. We obtained fastq files for the third-party dataset GSE140345 from SRA using fastq-dump from the SRA toolkit. The reanalyzed samples were GSM4159650, GSM4159652, GSM4159654, GSM4159656, GSM4159658, GSM4159660, GSM4159591, GSM4159593, GSM4159678, GSM4159680, GSM4159682, GSM4159684, GSM4159686, GSM4159688, GSM4159601, GSM4159603, GSM4159605, GSM4159607, GSM4159609, GSM4159611, GSM4159613, and GSM4159615. Raw sequencing reads from the fastq files were quantified with Salmon, and Tximeta was used to summarize counts to the gene level.