Hydra single-cell RNA-sequencing

Published: 3 April 2020| Version 2 | DOI: 10.17632/ctdfn57ds2.2
Åsa Björklund


Pacemaker neurons exert control over neuronal circuit function by their intrinsic ability to generate rhythmic bursts of action potential. Recent work has identified rhythmic gut contractions in human, mice and hydra to be dependent on both neurons and the resident microbiota. However, little is known about the evolutionary origin of these neurons and their interaction with microbes. In this study, we identified and functionally characterized prototypical ANO/SCN/TRPM ion channel expressing pacemaker cells in the basal metazoan Hydra by using a combination of single-cell transcriptomics, immunochemistry, and functional experiments. Unexpectedly, these prototypical pacemaker neurons express a rich set of immune-related genes mediating their interaction with the microbial environment. Functional experiments validated a model of the evolutionary emergence of pacemaker cells as neurons using components of innate immunity to interact with the microbial environment and ion channels to generate rhythmic contractions. Data includes: Full count matrices for all the plates: - SS_038.rsem_counts.txt.gz - SS_039.rsem_counts.txt.gz - SS_040.rsem_counts.txt.gz Full expression matrix after cell filtering: raw_count_table_seurat_filter_cluster_ID_191009_SG.txt.gz Metadata with cluster assignment: cell_seurat_clusters_identity.txt.gz


Steps to reproduce

Reads were mapped to Hydra transcriptome with Star and gene expression estimated with RSEM. Cells were clustered using Seurat. Details in methods section of paper - add link. All raw reads for the data are depsited at SRA: PRJNA614614 and PRJNA614611. Transcriptome sequence for Hydra vulgaris is deposited at SRP133389.


Karolinska Institutet, Christian-Albrechts-Universitat zu Kiel


Hydra, Messenger RNA