Sequencing of rapamycin-treated yeast strains across genetic backgrounds, with and without U18

This analysis covers the transcriptomes of four yeast strains (NA, WA, WE, and SA) under two rapamycin-based conditions: rapamycin (an autophagy inducer) alone, and rapamycin combined with U18666A (an Ncr1p inhibitor). Overall design: RNA-seq profiling of four yeast strains (DBVPG6044 [West African, “WA”: Mat alpha ho::NatMX, ura3::KanMXY12], Y12 [Sake, “SA”: Mat alpha ho::NatMX, ura3::KanMX], YPS128 [North American, “NA”: Mat alpha ho::NatMX, ura3::KanMX], and DBVPG6765 [Wine/European, “WE”: Mat alpha ho::NatMX, ura3::KanMX]). Samples were generated under two treatment conditions: rapamycin alone and rapamycin combined with U18666A. Rapamycin was used at 0.25 nM. Yeast cultures were grown in triplicate at 28°C to mid-log phase (OD600 ~0.8) in YNB medium (rapamycin-only condition) or YNB medium supplemented with U18666A (200 µg/mL) (rapamycin + U18666A condition). Cells were centrifuged and treated with zymolyase (2 U) for 30 minutes at 37°C. Total RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), followed by DNase I treatment (Promega) to remove genomic DNA. RNA integrity was verified using a Fragment Analyzer (Agilent).