Transcriptomics and epigenomics of Drosophila melanogaster fed on yeast mutant diets
[Whole-body RNA-seq] D. melanogaster larvae were fed on a control yeast strain (BY4741) or a nat3 yeast mutant strain, and the eclosed adults were subsequently reared on a common laboratory standard food. RNA was extracted from whole bodies of these wandering 3rd larvae, young adults (1 week old) and midlife adults (5 weeks old), and sequenced in single-end mode, respectively. [CUT&RUN sequencing] Larvae were fed on the respective yeast diets or subject to RNAi (with/without knocking down Gcn5; Gcn5 KD+/-, respectively). Then, dissected larvae were incubated with an anti-H3K9ac or IgG antibody. The larval DNA was cleaved, isolated, and sequenced in paired-end mode. [RNA-seq of larval CNS and adult brains] Central nervous system (CNS) was dissected from wandering 3rd larvae, which had been fed on the yeast diets or subjected to the knockdown. In addition, brains were dissected from 3-week-old adults that had acquired either the yeast diet history or the knockdown history in larval stages. RNA was extracted from individual samples and sequenced in single-end mode.