Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

Flatworms of the species Schmidtea mediterranea are immortal –adult animals contain a large pool of pluripotent stem cells that continuously differentiate to all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. Here, by combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a novel lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment. We characterize gene expression changes during differentiation and discover cell types important for regeneration. Our results demonstrate the importance of single-cell transcriptome analysis for mapping and reconstructing fundamental processes of developmental and regenerative biology at unprecedented resolution. Overall design: Single cell sequencing by drop-seq of Schmidtea mediterranea whole cells including 2 bulk population wild type samples fixed in methanol, 1 bulk population wild type sample cryopreserved, 2 bulk population wild type alive sample and 2 bulk population after control and Smed-h2b RNAi samples fixed in methanol and 3 wt samples at 3 different regeneration time points (day 0, day 2, day 4) fixed in methanol.