Code for the paper "Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity"

Update: the paper now is out in Nature Biotechnology

Code for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells. AnnData and conos objects are available from Zenodo repository (https://doi.org/10.5281/zenodo.6656930).

Content

• ipynb_notebooks contains .ipynb Jupyter notebooks:
  • 00_Data_preparation.ipynb: QC and creation of AnnData objects for the further analysis (view),
  • 01_Murine_thymus.ipynb: analysis of murine thymus composition (view),
  • 02_Human_thymus.ipynb: analysis of human thymus composition (view),
  • 03_Cross_species_alignment.ipynb: comparative analysis of murine and human thymic mesenchymal cells and validation of MC cell types on public data (view),
  • 04_Velocity_analysis.ipynb: RNA velocity analysis of Postn+ and Penk+ MCs from murine thymus (view),
  • 05_Bornstein_alignment.ipynb: validation of MC cell types on public data (view),
  • 06_Beta_regression.ipynb: some statistical computations (view),
  • 07_Figures.ipynb: figures preparation (view);
• tools contains additional functions that are used in Jupyter notebooks.

Citation

@article{Gustafsson2025Mesenchymal,
	author = {Gustafsson, Karin and Isaev, Sergey and Mirsanaye, Kamdin and Hofmann, Johanna and Kooshesh, Kameron A. and Baryawno, Ninib and Kiem, Anna and Severe, Nicolas and Zhao, Ting and Scadden, Elizabeth W. and Spencer, Joel A. and Burns, Christian and Akilan, Kumaran and Barkas, Nikolaos and Gessessew, Hayalneh and Kokkaliaris, Konstantinos D. and Lin, Charles P. and Kharchenko, Peter V. and Scadden, David T.},
	journal = {Nature Biotechnology},
	doi = {10.1038/s41587-025-02864-w},
	issn = {1087-0156},
	year = {2025},
	month = {oct 30},
	publisher = {{Springer Science and Business Media LLC}},
	title = {Mesenchymal thymic niche cells enable regeneration of the adult thymus and {T} cell immunity},
	url = {http://dx.doi.org/10.1038/s41587-025-02864-w},
}