April 10, 2023 Dataset Open Access

Kylies, Dominik; Zimmermann, Marina; Haas, Fabian; Schwerk, Maria; Kuehl, Malte; Brehler, Michael; Czogalla, Jan; Hernandez, Lola C.; Konczalla, Leonie; Okabayashi, Yusuke; Menzel, Julia; Edenhofer, Ilka; Mezher, Sam; Aypek, Hande; Dumoulin, Bernhard; Wu, Hui; Hofmann, Smilla; Kretz, Oliver; Wanner, Nicola; Tomas, Nicola M.; Krasemann, Susanne; Glatzel, Markus; Kuppe, Christoph; Kramann, Rafael; Banjanin, Bella; Schneider, Rebekka K.; Urbschat, Christopher; Arck, Petra; Gagliani, Nicola; van Zandvoort, Marc; Wiech, Thorsten; Grahammer, Florian; Sáez, Pablo J.; Wong, Milagros N.; Bonn, Stefan; Huber, Tobias B,; Puelles, Victor G.

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{"@context":"https://schema.org/","@id":"http://doi.org/10.25592/uhhfdm.11224","@type":"Dataset","creator":[{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Research Center On Rare Kidney Diseases (RECORD), University Hospital Erlangen, Erlangen, Germany.","name":"Kylies, Dominik"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Zimmermann, Marina"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Haas, Fabian"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Schwerk, Maria"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Kuehl, Malte"},{"@type":"Person","affiliation":"Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Brehler, Michael"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Czogalla, Jan"},{"@type":"Person","affiliation":"Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany","name":"Hernandez, Lola C."},{"@type":"Person","affiliation":"Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Konczalla, Leonie"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Division of Nephrology and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan","name":"Okabayashi, Yusuke"},{"@type":"Person","affiliation":"Abberior Instruments GmbH, G\u00f6ttingen, Germany","name":"Menzel, Julia"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Edenhofer, Ilka"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Mezher, Sam"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Aypek, Hande"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Dumoulin, Bernhard"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Wu, Hui"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Hofmann, Smilla"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Kretz, Oliver"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Wanner, Nicola"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Tomas, Nicola M."},{"@type":"Person","affiliation":"Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Krasemann, Susanne"},{"@type":"Person","affiliation":"Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Glatzel, Markus"},{"@type":"Person","affiliation":"Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany","name":"Kuppe, Christoph"},{"@type":"Person","affiliation":"Institute of Experimental Medicine and Systems Biology and Division of Nephrology and Clinical Immunology, RWTH Aachen University Medical Faculty, Aachen, Germany","name":"Kramann, Rafael"},{"@type":"Person","affiliation":"Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands and Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands","name":"Banjanin, Bella"},{"@type":"Person","affiliation":"Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands, Oncode Institute, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands and Institute for Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany","name":"Schneider, Rebekka K."},{"@type":"Person","affiliation":"Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Urbschat, Christopher"},{"@type":"Person","affiliation":"Department of Obstetrics and Fetal Medicine, Division of Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Arck, Petra"},{"@type":"Person","affiliation":"Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Gagliani, Nicola"},{"@type":"Person","affiliation":"Department of Genetics and Cell Biology, Maastricht University, School for Oncology and Reproduction GROW, School for Mental Health and Neuroscience MHeNS, and School for Cardiovascular Diseases CARIM, Maastricht University, Maastricht, The Netherlands and Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany","name":"van Zandvoort, Marc"},{"@type":"Person","affiliation":"Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Wiech, Thorsten"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Grahammer, Florian"},{"@type":"Person","affiliation":"Cell Communication and Migration Laboratory, Department of Biochemistry and Molecular Cell Biology (IBMZ), Center for Experimental Medicine, Hamburg, Germany","name":"S\u00e1ez, Pablo J."},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark and Department of Pathology, Aarhus University Hospital, Aarhus, Denmark","name":"Wong, Milagros N."},{"@type":"Person","affiliation":"Institute of Medical Systems Biology, Center for Biomedical AI (bAIome), Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Bonn, Stefan"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany","name":"Huber, Tobias B,"},{"@type":"Person","affiliation":"III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark and Department of Pathology, Aarhus University Hospital, Aarhus, Denmark","name":"Puelles, Victor G."}],"datePublished":"2023-04-10","description":"<p>Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems. However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF), has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies.</p>","distribution":[{"@type":"DataDownload","contentUrl":"https://www.fdr.uni-hamburg.de/api/files/c2d0cbaa-3916-4d14-884d-c628dcaee414/ext fig 10 3.png","encodingFormat":"png"},{"@type":"DataDownload","contentUrl":"https://www.fdr.uni-hamburg.de/api/files/c2d0cbaa-3916-4d14-884d-c628dcaee414/ext fig 10 4.png","encodingFormat":"png"},{"@type":"DataDownload","contentUrl":"https://www.fdr.uni-hamburg.de/api/files/c2d0cbaa-3916-4d14-884d-c628dcaee414/ext fig 10 ExSRRF 0.25 downscale-1.tif","encodingFormat":"tif"},{"@type":"DataDownload","contentUrl":"https://www.fdr.uni-hamburg.de/api/files/c2d0cbaa-3916-4d14-884d-c628dcaee414/ext fig 10 ExSRRF 0.25 downscale 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