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


  • M. Plass
  • J. Solana
  • F.A. Wolf
  • S. Ayoub
  • A. Misios
  • P. Glažar
  • B. Obermayer
  • F.J. Theis
  • C. Kocks
  • N. Rajewsky


  • Science


  • Science 360 (6391): eaaq1723


  • Flatworms of the species 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. By combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a 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 high resolution.