bulkRNA-Seq of tomato: seeding leaf
Leaf tissue samples from the basal region of young tomato leaves were collected using the same strategy as for spatial and single-nuclei datasets. Three biological replicates were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was extracted with Trizol reagent (Invitrogen) per the manufacturer's protocol. RNA quality was checked using NanoDrop 2000 for purity/concentration and Agilent 2100 Bioanalyzer for integrity (RIN  7.0 required).Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). Poly-A mRNA was enriched with oligo-dT magnetic beads, fragmented in First Strand Synthesis Reaction Buffer with divalent cations at elevated temperature, followed by second-strand cDNA synthesis and purification. Libraries were sequenced on Illumina NovaSeq 6000 to generate 150 bp paired-end reads.