WT C57BL/6J mice (males, aged between 8 and 12 wk) were used for SCN tissue collection as described by Jagannath et al. (2013) (link) at six distinct time points, starting from ZT3, at every 4 h, with lights on at 7 am (ZT0) and lights off at 7 pm (ZT12). We also collected cortical punches at ZT3 and ZT15 to compare and establish SCN-enriched chromatin modifications. An approximately 1-mm-thick mouse brain slice was sectioned between Bregma −0.1 and −1.0 mm using a brain matrix (Kent Scientific) and sterilized razor blades. The dissected mouse brain slice was placed on a cold block and promptly checked under a light microscope for the SCN (Bregma −0.3 and −0.8 mm, rostral to caudal) using cell-density contrast. Thereafter, the SCN (and cortex) was collected using a sample corer (1-mm internal diameter, Fine Science Tools) from the brain slice, flash-frozen on dry ice, and stored at −80°C. For histone ChIP, two separate biological replicates per time point per tissue type were collected, where each biological replicate comprised three to four individual SCN or cortical punches. For SCN-bulk RNA-seq, four biological replicates per time point were collected. Likewise, each biological replicate constituted three to four individual SCN samples.
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