“Stem cell differentiation trajectories in Hydra resolved at single-cell resolution” was published today in Science! This work was a collaboration between Jeff and the lab of Celina Juliano, including Stefan Siebert, Jack Cazet, Yash Abeykoon, and Abby Primack.

Adult Hydra continually renew all cells from three distinct stem cell populations. We sequenced 25,000 cells from adult Hydra and used URD to construct the differentiation trajectories of all cell types and identified the transcription factors expressed along each trajectory. Surprisingly, we found that neurons and gland cells transit through a common progenitor state, and characterized the full complement of neurons, providing the first genetic handles for the endodermal nerve net.

This work demonstrated the applicability of URD in multiple contexts, including in a case where there was no prior knowledge of cells’ temporal sequence. URD version 1.1 accompanied this paper, and included new functions for using NMF module analysis to detect and remove doublets, new functions for looking at gene expression relative to pseudotime, and new plotting functions for inspecting data.

Also, check out the perspective articles describing the work, including “The cells of regeneration” and “Looking at Hydra cells one at a time”.