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We used mRNA-seq to identify the RNA profiles in three tissue types (fat body, head and ovary) in two time points (after 10% cohort death (RNA-1) and 60% cohort death (RNA-2)) for two treatments (medium-quality larval diet (M) and high-quality larval diet (H)), with three biological replicates per tissue/time point/treatment combination. This data is NERC-funded but not held by the EIDC. This data is archived in the National Centre for Biotechnology Information, Gene Expression Omnibus (NCBI GEO).