Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease

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Acknowledgement

Work in APM’s and LC’s laboratory was supported by a Broad Innovation Grant from the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at the University of Southern California and a grant from the NIH to APM (NIDDK UC2DK126024). Additional support from the German Research Foundation grant GE 3179/1-1 (L.M.S.G.) and German Society of Internal Medicine (DGIM) Clinician Scientist grant (L.M.S.G.). The authors thank Inna-Marie Strazhnik for help with figure illustration and design.

Data Availability

The raw and processed data generated in this study were deposited in the Dryad database (https://datadryad.org/stash/dataset/doi:10.5061/dryad.bnzs7h4hj) and Zenodo (https://doi.org/10.5281/zenodo.12709329). The codebooks and probe sequences used to generate seqFISH probes used in this study are available as Supplementary Data 2 and 3. The probe sequences used to generate serial probes are available as Supplementary Data 4. Processed data can be browsed interactively at https://woldlab.caltech.edu/ci2-celltiles/Mouse-Kidney-Fibrosis/. Mouse sequencing data generated by Ransick et al. and by Kirita et al. and used in this study are available on GEO with accessions GSE129798 and GSE139107. Mouse T cell expression profiles were obtained from figshare (https://figshare.com/articles/dataset/ProjecTILs_murine_reference_atlas_of_tumor-infiltrating_T_cells_version_1/12478571/2). Human sequencing data was obtained from cellxgene (https://cellxgene.cziscience.com/collections/bcb61471-2a44-4d00-a0af-ff085512674c). Source data are provided with this paper.

Code Availability

Scripts used for processing seqFISH images can be found in GitHub (https://github.com/CaiGroup/pyfish_tools) and Zenodo (https://doi.org/10.5281/zenodo.12192195).

Additional Information