Whole flies were frozen and adult heads were isolated using brass sieves. Tissue was homogenized on ice, filtered to remove debris, and centrifuged on a sucrose cushion to isolate nuclei.
Flies were entrained under 12hr:12hr light:dark cycles for 3-4 days.
Total RNA was extracted from isolated nuclei using Trizol. Replicate 1 was depleted of ribosomal RNA, replicate 2 was not. For both replicates, mRNA was depleted by two rounds of poly(A) RNA depletion. Sequencing library was constructed per standard Illumina protocol.
