Abstract We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica , and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, wh ole a nimal, m ultiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.

Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity ofClytiaMedusa Cell Types