An ancestry-resolved ancient allopolyploid reveals integrated, homoeolog-partitioned immune regulation

This dataset contains RNA-seq raw counts and TPM-normalized expression matrices from Cucurbita moschata and its parental lineage representatives, sampled across infection time courses. Each time point includes three biological replicates. Metadata provide sample ID, species, time point, and replicate information. The dataset also includes differential expression results and analysis scripts used to generate figures in the study. These data enable users to investigate subgenome-resolved expression dynamics, copy-number-aware regulatory patterns, and immune responses in an ancient allopolyploid system.