A Synergy of Spatiotemporal Transcriptomic Techniques for Non-Model Organism Studies: Something Old, Something New, Something Borrowed, Something Ocean Blue

  • Kelly Watson

Student thesis: Master's Thesis


In situ hybridization (ISH) has played a crucial role in developing a spatial transcriptomic understanding of emerging model organisms in the past, but advancing high-throughput RNA-sequencing (RNA-seq) technology has pushed this method into the shadows, leading to a loss of data resolution. This shift in research towards the exclusive use of RNA-seq neglects essential considerations for transcriptomic studies including the spatial and temporal expression of transcripts, available budget, experimental design needs, and validation of data. A synergy of spatiotemporal transcriptomic techniques is needed, using the bulk and unbiased analysis of RNA-seq and the visual validation and spatiotemporal resolution of ISH. Integration of this synergistic approach can improve our molecular understanding of non-model organisms and establish the background data needed for advancing research techniques. A prime example lies within an emerging model of the marine science and symbiosis fields, where I present a case study on a threatened coral reef keystone – the cnidarian-dinoflagellate symbiosis. Establishing a whole-mount ISH protocol for the emerging cnidarian model Aiptasia (sea anemone) will help future studies reveal the gene regulation underpinning the establishment, persistence, and breakdown of this complex symbiotic relationship.
Date of AwardJul 2021
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorManuel Aranda (Supervisor)


  • in situ hybridization
  • RNA-sequencing
  • spatiotemporal transcriptomics
  • non-model organisms
  • corals
  • cnidarian-dinoflagellate symbiosis

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