GSM9289252: EDS615, ltv1∆/ltv1∆, experimental, replicate 1; Saccharomyces cerevisiae S288C; RNA-Seq
RNA was extracted using the hot phenol method. Cells were grown to mid-exponential phase (OD600 0.5–0.6), pelleted, washed twice with ddH2O, and stored at -80°C. Pellets were resuspended in buffer (50 mM sodium acetate, 10 mM EDTA, 1% SDS, pH 5.2), mixed with hot phenol (65°C), vortexed, incubated at 65°C for 5 min with periodic inversion, and centrifuged at 15,000 x g for 5 min. Aqueous phase was collected and re-extracted with phenol:chloroform, followed by ethanol precipitation, 70% ethanol washes, air-drying, and resuspension in RNase-free water. RNA quality and concentration were checked by OD260/280 and 1% agarose gel electrophoresis. Batch-Tag-Sequencing (Batch-Taq-Seq) libraries were prepared at the UC Davis Genome Center with inline UMIs and sample indexes for multiplexing. Sequencing used single-end 84–90 cycle chemistries on NextSeq 500 instruments, generating ~3–6 million reads per sample. The core returned only reads passing Illumina quality filters.