Genome Biology (Mar 2024)
FixNCut: single-cell genomics through reversible tissue fixation and dissociation
- Laura Jiménez-Gracia,
- Domenica Marchese,
- Juan C. Nieto,
- Ginevra Caratù,
- Elisa Melón-Ardanaz,
- Victoria Gudiño,
- Sara Roth,
- Kellie Wise,
- Natalie K. Ryan,
- Kirk B. Jensen,
- Xavier Hernando-Momblona,
- Joana P. Bernardes,
- Florian Tran,
- Laura Katharina Sievers,
- Stefan Schreiber,
- Maarten van den Berge,
- Tessa Kole,
- Petra L. van der Velde,
- Martijn C. Nawijn,
- Philip Rosenstiel,
- Eduard Batlle,
- Lisa M. Butler,
- Ian A. Parish,
- Jasmine Plummer,
- Ivo Gut,
- Azucena Salas,
- Holger Heyn,
- Luciano G. Martelotto
Affiliations
- Laura Jiménez-Gracia
- Centro Nacional de Análisis Genómico (CNAG)
- Domenica Marchese
- Centro Nacional de Análisis Genómico (CNAG)
- Juan C. Nieto
- Centro Nacional de Análisis Genómico (CNAG)
- Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG)
- Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
- Victoria Gudiño
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
- Sara Roth
- Cancer Immunology Program, Peter MacCallum Cancer Centre
- Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide
- Natalie K. Ryan
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide
- Kirk B. Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide
- Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
- Joana P. Bernardes
- Institute of Clinical Molecular Biology, Kiel University
- Florian Tran
- Institute of Clinical Molecular Biology, Kiel University
- Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Kiel University
- Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University
- Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen
- Tessa Kole
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen
- Petra L. van der Velde
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen
- Martijn C. Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen
- Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University
- Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology
- Lisa M. Butler
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide
- Ian A. Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre
- Jasmine Plummer
- St Jude Children’s Research Hospital
- Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG)
- Azucena Salas
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
- Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG)
- Luciano G. Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide
- DOI
- https://doi.org/10.1186/s13059-024-03219-5
- Journal volume & issue
-
Vol. 25,
no. 1
pp. 1 – 36
Abstract
Abstract The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
Keywords
