cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17041980
title: Mechanical strain exacerbates Pseudomonas infection in an organoid-based pneumonia-on-a-chip model

description: 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. geraldine.nouailles@charite.de

 

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.
DOI: 10.5517/ccsjkkd
title: CCDC 730904: Experimental Crystal Structure Determination

description: Related Article: Bing Wang, Pei-Pei Zhang|2012|Tetrahedron Lett.|53|119|doi:10.1016/j.tetlet.2011.11.002
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwzmdv
title: CCDC 833788: Experimental Crystal Structure Determination

description: Related Article: R.Singh, M.Schober, Xiaodong Hou, A.Seay, Qianli Chu|2012|Tetrahedron Lett.|53|173|doi:10.1016/j.tetlet.2011.10.162
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccw5jzj
title: CCDC 809688: Experimental Crystal Structure Determination

description: Related Article: S.Paul, S.Pattanayak, S.Sinha|2011|Tetrahedron Lett.|52|6166|doi:10.1016/j.tetlet.2011.09.040
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwzmfw
title: CCDC 833789: Experimental Crystal Structure Determination

description: Related Article: R.Singh, M.Schober, Xiaodong Hou, A.Seay, Qianli Chu|2012|Tetrahedron Lett.|53|173|doi:10.1016/j.tetlet.2011.10.162
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccw5k0l
title: CCDC 809689: Experimental Crystal Structure Determination

description: Related Article: S.Paul, S.Pattanayak, S.Sinha|2011|Tetrahedron Lett.|52|6166|doi:10.1016/j.tetlet.2011.09.040
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx9jk8
title: CCDC 843310: Experimental Crystal Structure Determination

description: Related Article: P.Wessig, R.Wawrzinek, K.Mollnitz, E.Feldbusch, U.Schilde|2011|Tetrahedron Lett.|52|6192|doi:10.1016/j.tetlet.2011.09.058
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwyg08
title: CCDC 832660: Experimental Crystal Structure Determination

description: Related Article: V.A.Mamedov, N.A.Zhukova, T.N.Beschastnova, E.I.Zakirova, S.F.Kadyrova, E.V.Mironova, A.G.Nikonova, S.K.Latypov, I.A.Litvinov|2012|Tetrahedron Lett.|53|292|doi:10.1016/j.tetlet.2011.11.013
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx2lr9
title: CCDC 836651: Experimental Crystal Structure Determination

description: Related Article: S.Nandi, J.K.Ray|2011|Tetrahedron Lett.|52|6203|doi:10.1016/j.tetlet.2011.09.070
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwpbkf
title: CCDC 824865: Experimental Crystal Structure Determination

description: Related Article: J.Taesch, T.T.Dang, V.Heitz|2012|Tetrahedron Lett.|53|333|doi:10.1016/j.tetlet.2011.11.045
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwyg19
title: CCDC 832661: Experimental Crystal Structure Determination

description: Related Article: V.A.Mamedov, N.A.Zhukova, T.N.Beschastnova, E.I.Zakirova, S.F.Kadyrova, E.V.Mironova, A.G.Nikonova, S.K.Latypov, I.A.Litvinov|2012|Tetrahedron Lett.|53|292|doi:10.1016/j.tetlet.2011.11.013
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.23621.42727
title: Magnitude and Direction Asymmetries Isokinetic Torque of Swimmers
DOI: 10.5281/zenodo.17406797
title: Benchmark Boolean Models for Gene Regulatory Networks

description: Gene regulatory networks (GRNs) capture the processes involved in gene regulation. Boolean network (BN) modeling provides a simple but effective framework for understanding the dynamical behavior of GRNs. Although BNs have been widely studied and applied, algorithms and theoretical analyses are usually tested on ad hoc models, which may introduce bias and fail to capture the properties of real GRNs. Benchmarking offers standardized models for validation and comparison. We construct benchmark BN models for GRNs of four major biological kingdoms: animals, bacteria, fungi, and plants. All models are built from empirically observed recurrent properties and motifs in GRNs. The proposed benchmark BNs provide a basis for evaluating algorithms and theoretical analyses.
DOI: 10.5517/ccsddg0
title: CCDC 726902: Experimental Crystal Structure Determination

description: Related Article: Lili Feng, P.H. Karpinski, P. Sutton, Yugang Liu, D.F. Hook, Bin Hu, T.J. Blacklock, P.E. Fanwick, M. Prashad, S. Godtfredsen, C. Ziltener|2012|Tetrahedron Lett.|53|275|doi:10.1016/j.tetlet.2011.11.029
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwpblg
title: CCDC 824866: Experimental Crystal Structure Determination

description: Related Article: J.Taesch, T.T.Dang, V.Heitz|2012|Tetrahedron Lett.|53|333|doi:10.1016/j.tetlet.2011.11.045
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccxdt58
title: CCDC 846460: Experimental Crystal Structure Determination

description: Related Article: C.J.A.Ribeiro, S.P.Kumar, R.Moreira, M.M.M.Santos|2012|Tetrahedron Lett.|53|281|doi:10.1016/j.tetlet.2011.10.139
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.12925.95201
title: Neues_Lernen_Chatbot-Didaktik.pdf
DOI: 10.5517/ccwxt4q
title: CCDC 832044: Experimental Crystal Structure Determination

description: Related Article: Junfeng Wang, Qin Li, Zemei Ge, Runtao Li|2012|Tetrahedron|68|1315|doi:10.1016/j.tet.2011.11.029
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx994m
title: CCDC 843080: Experimental Crystal Structure Determination

description: Related Article: M.Tomar, N.T.Lucas, M.G.Gardiner, K.Mullen, J.Jacob|2012|Tetrahedron Lett.|53|285|doi:10.1016/j.tetlet.2011.11.008
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccx995n
title: CCDC 843081: Experimental Crystal Structure Determination

description: Related Article: M.Tomar, N.T.Lucas, M.G.Gardiner, K.Mullen, J.Jacob|2012|Tetrahedron Lett.|53|285|doi:10.1016/j.tetlet.2011.11.008
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwxt5r
title: CCDC 832045: Experimental Crystal Structure Determination

description: Related Article: Junfeng Wang, Qin Li, Zemei Ge, Runtao Li|2012|Tetrahedron|68|1315|doi:10.1016/j.tet.2011.11.029
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwszxj
title: CCDC 828379: Experimental Crystal Structure Determination

description: Related Article: V.Kavala, Chunchi Lin, Chun-Wei Kuo, Hulin Fang, Ching-Fa Yao|2012|Tetrahedron|68|1321|doi:10.1016/j.tet.2011.11.022
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwszyk
title: CCDC 828380: Experimental Crystal Structure Determination

description: Related Article: V.Kavala, Chunchi Lin, Chun-Wei Kuo, Hulin Fang, Ching-Fa Yao|2012|Tetrahedron|68|1321|doi:10.1016/j.tet.2011.11.022
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwnnfl
title: CCDC 824210: Experimental Crystal Structure Determination

description: Related Article: N.Asmafiliz, Z.Kilic, Z.Hayvali, L.Acik, T.Hokelek, H.Dal, Y.Oner|2012|Spectrochim.Acta,Part A|86|214|doi:10.1016/j.saa.2011.10.027
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwnngm
title: CCDC 824211: Experimental Crystal Structure Determination

description: Related Article: N.Asmafiliz, Z.Kilic, Z.Hayvali, L.Acik, T.Hokelek, H.Dal, Y.Oner|2012|Spectrochim.Acta,Part A|86|214|doi:10.1016/j.saa.2011.10.027
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwnnhn
title: CCDC 824212: Experimental Crystal Structure Determination

description: Related Article: N.Asmafiliz, Z.Kilic, Z.Hayvali, L.Acik, T.Hokelek, H.Dal, Y.Oner|2012|Spectrochim.Acta,Part A|86|214|doi:10.1016/j.saa.2011.10.027
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctl4n5
title: CCDC 762217: Experimental Crystal Structure Determination

description: Related Article: N.Ikpo, L.N.Saunders, J.L.Walsh, J.M.B.Smith, L.N.Dawe, F.M.Kerton|2011|Eur.J.Inorg.Chem.|2011|5347|doi:10.1002/ejic.201100703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccwwbgj
title: CCDC 830628: Experimental Crystal Structure Determination

description: Related Article: Zhen-Ju Jiang, Jin-Ting Liu, Hong-Shui Lv, Bao-Xiang Zhao|2012|Spectrochim.Acta,Part A|86|181|doi:10.1016/j.saa.2011.10.021
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17405143
title: TCR-DeepInsight Reference Datasets [Raw Count]

description: Additional datasets related to https://zenodo.org/records/12741480.Please cite the original Zenodo record: Ziwei Xue. (2025). TCR-DeepInsight Reference Datasets (v2.5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12741480
DOI: 10.5517/cctl4r8
title: CCDC 762220: Experimental Crystal Structure Determination

description: Related Article: N.Ikpo, L.N.Saunders, J.L.Walsh, J.M.B.Smith, L.N.Dawe, F.M.Kerton|2011|Eur.J.Inorg.Chem.|2011|5347|doi:10.1002/ejic.201100703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctl4s9
title: CCDC 762221: Experimental Crystal Structure Determination

description: Related Article: N.Ikpo, L.N.Saunders, J.L.Walsh, J.M.B.Smith, L.N.Dawe, F.M.Kerton|2011|Eur.J.Inorg.Chem.|2011|5347|doi:10.1002/ejic.201100703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.17041981
title: Mechanical strain exacerbates Pseudomonas infection in an organoid-based pneumonia-on-a-chip model

description: 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. geraldine.nouailles@charite.de

 

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.
DOI: 10.5281/zenodo.17404528
title: TCR-DeepInsight Reference Datasets [Raw Count]

description: Additional datasets related to https://zenodo.org/records/12741480.Please cite the original Zenodo record: Ziwei Xue. (2025). TCR-DeepInsight Reference Datasets (v2.5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12741480
DOI: 10.5517/cctl4tb
title: CCDC 762222: Experimental Crystal Structure Determination

description: Related Article: N.Ikpo, L.N.Saunders, J.L.Walsh, J.M.B.Smith, L.N.Dawe, F.M.Kerton|2011|Eur.J.Inorg.Chem.|2011|5347|doi:10.1002/ejic.201100703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cctl4vc
title: CCDC 762223: Experimental Crystal Structure Determination

description: Related Article: N.Ikpo, L.N.Saunders, J.L.Walsh, J.M.B.Smith, L.N.Dawe, F.M.Kerton|2011|Eur.J.Inorg.Chem.|2011|5347|doi:10.1002/ejic.201100703
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.