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Among the powerful tools for physiological omics is the study of RNA, where broad sequencing of RNA leads to hypothesis generation and testing while providing observational discovery. Emphasis has been placed on RNA molecules that code for proteins, even though they represent a minority of total RNA. Diverse sequencing methods have rapidly expanded the identification of non-protein-coding molecules, including nonsense-mediated decay and long non-coding RNAs (lncRNA), which now represent the most diverse class of RNA. Increasing attention needs to be paid to the data processing of RNA sequencing to interpret transcript-level mapping data in the context of protein biology, as many protein-coding genes have diverse noncoding transcripts. Over the past several years, single-cell and spatial transcriptomics have yielded unprecedented insights into cellular, tissue, and organ physiology. 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