ATAC-Seq of Mus musculus brain regions after sleep deprivations
C57Bl/6J mice, both males and females were maintained under a 12h/12h light/dark cycle and sleep deprived for 6h from lights on. Animals were sacrificed and brains isolated. Tissue punches (cortex, DG, SCN) were homogenized directly to nuclei by adopting the nuclei isolation protocol from Su et al. (Su et al., 2017) with slight modifications (using a dounce homogenizer and sucrose cushion). The viability of nuclei was then checked under a microscope using ThermoFisher NucBlue Live ReadyProbes reagent. Following successful isolation of intact nuclei, ATAC-seq libraries were prepared using the Tn5 transposase. Typically, nuclei from 4 punches, containing approximately 40,000 nuclei were re-suspended in the transposition mix (25L 2x TD Buffer (Illumina Cat no. FC-121-1030), 2.5L Tn5 Transposes (Illumina Cat no. FC-121-1030) and 22.5L nuclease free water) and incubated at 37C for 30 min. DNA was then purified using the Qiagen MinElute Kit and eluted with 23L warm 10mM Tris, pH8 and stored at -20C.  The transposed DNA was finally amplified using Nextera sequencing primers, quantified and sequenced at Illumina NextSeq 500 platform.