Input files used in scripts

Version 1

Input Files for Manuscript "A pulmonologist’s guide to perform and analyse cross-species single-lung-cell transcriptomic"

See https://github.com/GenStatLeipzig/pulmonologists_interspecies_scRNA for details.

Manuscript authored by:

Peter Pennitz1,2*, Holger Kirsten3*, Vincent D. Friedrich3,4, Emanuel Wyler5, Cengiz Goekeri1,2,6, Benedikt Obermayer7, Gitta A. Heinz8, Mir-Farzin Mashreghi8,9, Maren Büttner10,11 Jakob Trimpert12, Markus Landthaler5,13, Norbert Suttorp2, Andreas C. Hocke1,2, Stefan Hippenstiel2, Mario Tönnies14, Markus Scholz3, Wolfgang M. Kuebler15,16, Martin Witzenrath1,2,16, Katja Hoenzke1,2 and Geraldine Nouailles1,2,#

1 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Division of Pulmonary Inflammation, Berlin, Germany.

2 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.

3 University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.

4 Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany.

5 Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.

6 Cyprus International University, Faculty of Medicine, Nicosia, Cyprus.

7 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany.

8 Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany.

9 Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany.

10 University of Bonn, Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, Bonn, Germany.

11 Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Systems Medicine, Bonn, Germany.

12 Freie Universität Berlin, Institute of Virology, Berlin, Germany.

13 Humboldt-Universität zu Berlin, Institute for Biology, IRI Life Sciences, Berlin, Germany.

14 HELIOS Clinic Emil von Behring, Department of Pneumology and Department of Thoracic Surgery, Chest Hospital Heckeshorn, Berlin, Germany.

15 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Physiology, Berlin, Germany.

German Center for Lung Research (DZL), Berlin, Germany.

• Authors contributed equally to this work

References for original datasets :

Human Charité: Hocke A, Hönzke K, Obermayer B, Baumgardt M, Wyler E, Hippenstiel S, Mache C. Charité Berlin /Berlin Institute of Health. GEO accessions GSM5958267, GSM5958272, GSM5958283, GSM5958285

Human Travaglini et al.: published at https://www.synapse.org by Travaglini et al. (https://doi.org/10.1038/s41586-020-2922-4 Titel anhand dieser DOI in Citavi-Projekt übernehmen)

Monkey: published at https://www.ncbi.nlm.nih.gov/geo by Speranza et al. (https://doi.org/10.1126/scitranslmed.abe8146 Titel anhand dieser DOI in Citavi-Projekt übernehmen)

Hamster: Charité Berlin, see: https://doi.org/10.1038/s41467-021-25030-7 Titel anhand dieser DOI in Citavi-Projekt übernehmen

Mouse: Pennitz P, Witzenrath, M, Nouailles G, Berlin Charité.

Rat and Pig: published at https://www.ncbi.nlm.nih.gov/geo by Raredon et al. (https://doi.org/10.1126/sciadv.aaw3851 Titel anhand dieser DOI in Citavi-Projekt übernehmen) .

Annotation: Ensembl BioMart