Expression profiling by high throughput sequencing
We used a systems genetics approach in the BXD genetic reference population of mice and assembled a comprehensive experimental knowledge base comprising a deep ‘sleep-wake’ phenome, central and peripheral transcriptomes, and plasma metabolome data, collected under undisturbed baseline conditions and after sleep deprivation.
We subjected mice from 33 BXD/RwwJ lines, 4 BXD/TyJ, the two parental strains (B6 and D2), as well as F1 individuals from reciprocal crosses between the parental lines, to a deep behavioral and molecular phenotyping with steady-state RNA levels in brain and liver under control and sleep deprivation. Sleep deprivation was performed during 6h (ZT0-6), animals were sleep deprived in their home cage by “gentle handling” . Half of the animals were sleep deprived (SD), the other half was left undisturbed in another room (i.e., control or Ctr). Both SD and Ctr mice were sacrificed at ZT6, i.e., immediately after the end of the SD, for sampling of liver and cerebral cortex tissue. The mice initially sacrificed for tissue collection yielded to 277 cortex and 277 liver samples of good quality. Equal amounts of RNA from biological replicates (same strain/line and experimental condition) were pooled. In addition, to assess the stability of outcome variables over time, parental lines were sampled twice; i.e., at the start (labelled B61 and DB1) and end (labelled B62 and DB2) of the breeding and data-collecting phase which spanned 2 years (March 2012- December 2013). In summary we generated 172 RNA-seq data sets.