Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury

Christian Hinze^1,2,3, Christine Kocks⁴, Janna Leiz^2,3, Nikos Karaiskos⁴, Anastasiya Boltengagen⁴, Shuang Cao^1,2,3, Christopher Mark Skopnik^2,5, Jan Klocke^2,5,6, Jan-Hendrik Hardenberg², Helena Stockmann², Inka Gotthardt², Benedikt Obermayer⁷, Laleh Haghverdi⁴, Emanuel Wyler⁴, Markus Landthaler⁴, Sebastian Bachmann⁸, Andreas C. Hocke^6,9, Victor Corman¹⁰, Jonas Busch¹¹, Wolfgang Schneider¹², Nina Himmerkus¹³, Markus Bleich¹⁴, Kai-Uwe Eckardt^2,*, Philipp Enghard^2,5,*, Nikolaus Rajewsky^4,*, Kai M. Schmidt-Ott<sup>1,2,3,*,#

1</sup> Department of Nephrology and Hypertensiology, Hannover Medical School, Hannover, Germany.
² Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
³ Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
⁴ Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, Berlin, Germany.
⁵ Deutsches Rheumaforschungszentrum, an Institute of the Leibniz Foundation, Berlin, Germany.
⁶ Berlin Institute of Health, Berlin, Germany.
⁷ Core Unit Bioinformatics, BIH/Charité/MDC, Berlin, Germany.
⁸ Institute for Functional Anatomy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
⁹ Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
¹⁰ Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
¹¹ Department of Urology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
¹² Department of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
¹³ Institute of Physiology, Christian-Albrechts-Universität, Kiel, Germany.
^* Senior authors.
^# Corresponding author.

This interface was created and is maintained by Christian Hinze.

Features

The following features are currently supported in the atlas:

• The 'Overview' tab provides (from left to right) 1.) the original UMAP plot from Fig. 1 of the paper, 2.) a feature plot showing a selected gene's expression on the UMAP plot and 3.) a bar plot showing gene expression as counts per million (CPM) value for the selected gene within each of the major cell types. CPM values were calculated separately for each major cell type.
• Additional tabs show subclusterings of major cell types (as indicated). Each tab provides (from left to right) 1.) a scatter plot of gene expression per individual (CPM) comparing control individuals versus AKI individuals, 2.) the original UMAP plot of the subclustering from the paper, 3.) a feature plot of the selected gene projected onto the UMAP, and 4.) a bar plot showing the expression of the selected gene (CPM) within each subcluster, 5.) individual feature plots for control and AKI samples.

Release notes

• 14-Jun-22: revised version uploaded.