Planaria Single Cell Atlas

PSCA is developed by the Rajewsky lab at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center in Berlin.

PSCA supplements the following publication (free access [full text] [pdf]):

Cell Type Atlas and Lineage Tree of a Whole Complex Animal by Single-Cell Transcriptomics

      Mireya Plass1,†, Jordi Solana1,†‡, F. Alexander Wolf2, Salah Ayoub1, Aristotelis Misios1, Petar Glažar1,
      Benedikt Obermayer1,⊺, Fabian J. Theis2,3, Christine Kocks1, and Nikolaus Rajewsky1,*

      1 Systems Biology of Gene Regulatory Elements, BIMSB, MDC
      2 Helmholtz Zentrum München, German Research Center for Environmental Health,
      Institute of Computational Biology, Neuherberg, Germany
      3 Department of Mathematics, Technische Universität München, Germany
       Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
       Present address: Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
      * Corresponding author
       These authors contributed equally to the work

      Science 360 (6391), eaaq1723
      DOI: 10.1126/science.aaq1723

      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 adults 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 group.
      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

Correspondence regarding the publication: Nikolaus Rajewsky

PSCA-related questions: Petar Glažar


PSCA currently offers the following features:

  • t-SNE: a two-dimensional representation of the S. mediterranea cell atlas, showing the cell type populations identified and allowing to display the expression values of individual genes on the t-SNE. Additionally, we provide a browsable table including all the marker genes identified for each cell cluster.

  • lineage: representation of gene expression changes in pseudotemporally ordered cells of any of the detected lineages and on the tree.

  • regeneration: violin plots showing the expression levels per cluster in WT and regeneration samples.

  • downloads: download additional files to reproduce the analyses performed in the paper included in as well as additional processed files.

Release notes

  • 2018-02-13 early access enabled

Files for reproducing PAGA analyses:


       PC values calculated with Seurat for each cell used in the PAGA analysis.


       Cell type annotation for each cell used in the PAGA analysis.


       Color names for each of the clusters used in the PAGA analysis.

Files for reproducing VELOCYTO analyses:


       annotation file used to perform velocyto analysis


       loom file containing the single-cell RNA-seq data used to perform velocyto analysis

other files:


       DGE matrix containing the expression values of all cells included in the paper.


       Pseudotime computed for each cell with PAGA. Cells are in the same order as in the dge matrix.