Single-cell RNA-seq Portal
The updated Hydra vulgaris single-cell RNA-seq portal, including both the whole-animal and neuron-enriched atlases, is now hosted by the Juliano Lab at https://cejuliano.shinyapps.io/HydraAtlas, using the shinyapps.io platform. Please direct all single-cell portal inquiries to the Juliano Lab and include "HVAEP scPortal:" in the subject line.
Project Overview
The adult Hydra polyp continuously renews its cells from three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. To uncover the transcriptional changes that occur as cells differentiate, we used Drop-seq to sequence the transcriptomes of approximately 25,000 single Hydra cells, which includes a broad spectrum of cell states, from stem cells to terminally differentiated cells (Siebert et al, 2019; Cazet et al, 2023). Additionally, we used 10X genomics to sequence the transcriptomes of approximately 35,000 neurons and neural progenitor cells (Little et al, 2025). This study provides a comprehensive transcriptional characterization of the adult Hydra nervous system, including trajectory analysis to describe the differentiation and transdifferentiation pathways used to make Hydra neurons. This portal presents these data in an interactive format and allows for the visualization of sequencing statistics, clustering results, and gene expression across every cell in both the whole animal and neuron datasets. In addition, the neuron dataset includes differentiation trajectories of each neuron subtype and allows for the visualization of gene expression across these trajectories.
- Siebert, S., Farrell, J.A., Cazet, J.F., Abeykoon, Y., Primack, A.S., Schnitzler, C.E., Juliano, C.E. Stem cell differentiation trajectories in Hydra resolved at single-cell resolution. Science. 2019 Jul 26, 365(6451): eaav9314. [PMCID: PMC7104783]
- Cazet, J.F., Siebert, S., Little, H.M., Bertemes, P., Primack, A.S., Ladurner, P., Achrainer, M., Fredriksen, M.T., Moreland, R.T., Singh, S., Zhang, S., Wolfsberg, T.G., Schnitzler, C.E., Baxevanis, A.D., Simakov, A., Hobmayer, B., and Juliano, C.E. A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state. Genome Research. 2023, 33: 283-298. [PMCID: PMC1006946]
- Morris Little, H., Primack, A.S., Tsverov, J., Nunneley, M.P., Mühlbauer, S., Cox, B.D., Busse, C., Schneid, S., Louwagie, A., Cazet, J.F., David, C.N., Farrell, J.A., Juliano, C.E. A molecular, spatial and regulatory atlas of the Hydra vulgaris nervous system. Development. 2025 Oct 24, 152(20): dev204983. [PMCID: PMC12860537]
