Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex

Supplemental Table S1. Genes from an independent microarray study or identified in previous literature that are known to be affected by sleep deprivation or recovery sleep and genes (empirical negative controls) unaffected by 5–6 hours of SD.

Supplemental Table S2. Recovery rates of positive and empirical negative control genes at SD5–6 for different expression level cutoffs on log2 counts per million (log2CPM).

Supplemental Table S3. All upregulated and downregulated differentially expressed genes (FDR < 0.05) for each of the four pairwise comparisons (treatment compared to home cage control).

Supplemental Table S4. Differentially expressed genes (FDR < 0.05 and log2CPM > 0) that are shared between time points or that are unique to certain sleep deprivation or recovery sleep time points. Each non-empty intersection is separated into upregulated and downregulated genes.

Supplemental Table S5. Results from functional enrichment analysis with DAVID for each intersection as well as the union (indicated by U) across SD3/SD5–6 and SD5–6 for each of the three patterns of recovery.