Mechanical strain exacerbates Pseudomonas infection in an organoid-based pneumonia-on-a-chip model

Online supplementary data including the seurat objects used in scRNA analysis AUTHORS: Karen Hoffmann1, Ulrike Behrendt1, Peter Pennitz1, Holger Kirsten2, Jessica Pohl3, Elena Lopez-Rodriguez4, Chantal Weissfuss1,3, Jens Kollmeier5, Mario Tönnies5, Sebastian Brill6, Konrad Steinestel6, Martin Witzenrath1, Werner Wenzel3, Christian Zobel3*, Geraldine Nouailles1* *shared 1 Charité - Universitätsmedizin Berlin, Department of Infectious Diseases, Respiratory Medicine and Critical Care, Berlin, Germany. 2 University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany 3 Bundeswehrkrankenhaus Berlin, Department of Internal Medicine and Department of Microbiology and Hospital Hygiene, Berlin, Germany. 4 Charité – Universitätsmedizin Berlin, Institute of Functional Anatomy, Berlin, Germany. 5 Respiratory Diseases Clinic Heckeshorn, Helios Klinikum Emil von Behring GmbH, Berlin, Germany. 6 Bundeswehrkrankenhaus Ulm, Department for Thoracic-Surgery and Institute of Pathology and Molecular Pathology, Ulm, Germany. Correspondence to: Geraldine Nouailles; Charitéplatz 1, 10117 Berlin, Germany. [e-mail] Support statement: We thank Jean-Marc Ghigo from the Institute Pasteur and a member of the “MAPVAP” consortium for kindly providing the PAO1-GFP strain to our lab. We thank Virginia Weber, Annette Daniel, and Ute Mauer for their valuable technical support. During the preparation of this work, the authors used ChatGPT / OpenAI, Grammarly / Grammarly, Inc. to improve English language and grammar, as well as German to English translations. After using these tools, the authors reviewed and edited the content as needed and take full responsibility for the content of the publication. Schematics were created with BioRender.com. This study was funded by the Department E of the Bundeswehr Medical Service Academy (SoFo 39K4), Ministry of Defence, Germany, and BAAINBw (E/U2ED/PD014/OF550). File description: 22_seurat_integrated.rds scRNA Seurat file from 10xV3, filtered and preprocessed and integrated, used for differential expression analysis as described in the manuscript and https://github.com/GenStatLeipzig/2412_scRNA_lung_organoid_chip. The object includes data from four experimental groups (CPAECs and ODAECs at 5% and 10% stretch) that have been quality controlled, filtered, and integrated using RPCA in Seurat v5. It also includes data integrated with a previously published dataset of alveolar organoids.