Cell type transcriptome atlas for the planarian Schmidtea mediterranea

Christopher T. Fincher^1,2,3, Omri Wurtzel^1,2, Thom de Hoog^1,2, Kellie M. Kravarik^1,2,3, Peter W. Reddien^1,2,3,*
Fincher et al., Science, Published online 19 April 2018

The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.

t-SNE embedding of 50,562 single planarian cells based on gene expression.

1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
2. Howard Hughes Medical Institute; Massachusetts Institute of Technology, Cambridge, MA 02139, USA
3. Department of Biology; Massachusetts Institute of Technology, Cambridge, MA 02139, USA
* Correspondence: reddien@wi.mit.edu

The planaria single-cell page is hosted by the Reddien lab @ The Whitehead Institute