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A Synergy of Spatiotemporal Transcriptomic Techniques for Non-Model Organism Studies: Something Old, Something New, Something Borrowed, Something Ocean BlueWatson, Kelly 07 1900 (has links)
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.
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