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FixNCut: single-cell genomics through reversible tissue fixation and dissociation.
Jiménez-Gracia, Laura; Marchese, Domenica; Nieto, Juan C; Caratù, Ginevra; Melón-Ardanaz, Elisa; Gudiño, Victoria; Roth, Sara; Wise, Kellie; Ryan, Natalie K; Jensen, Kirk B; Hernando-Momblona, Xavier; Bernardes, Joana P; Tran, Florian; Sievers, Laura Katharina; Schreiber, Stefan; van den Berge, Maarten; Kole, Tessa; van der Velde, Petra L; Nawijn, Martijn C; Rosenstiel, Philip; Batlle, Eduard; Butler, Lisa M; Parish, Ian A; Plummer, Jasmine; Gut, Ivo; Salas, Azucena; Heyn, Holger; Martelotto, Luciano G.
Affiliation
  • Jiménez-Gracia L; Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
  • Marchese D; Universitat de Barcelona (UB), Barcelona, Spain.
  • Nieto JC; Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
  • Caratù G; Universitat de Barcelona (UB), Barcelona, Spain.
  • Melón-Ardanaz E; Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
  • Gudiño V; Universitat de Barcelona (UB), Barcelona, Spain.
  • Roth S; Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
  • Wise K; Universitat de Barcelona (UB), Barcelona, Spain.
  • Ryan NK; Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
  • Jensen KB; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
  • Hernando-Momblona X; Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
  • Bernardes JP; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
  • Tran F; Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
  • Sievers LK; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
  • Schreiber S; Monash University Department of Surgery, Alfred Hospital, Melbourne, VIC, Australia.
  • van den Berge M; Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia.
  • Kole T; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
  • van der Velde PL; Australian Genomics Research Facility, Adelaide, South Australia, Australia.
  • Nawijn MC; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
  • Rosenstiel P; Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia.
  • Batlle E; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
  • Butler LM; Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia.
  • Parish IA; South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
  • Plummer J; Australian Genomics Research Facility, Adelaide, South Australia, Australia.
  • Gut I; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
  • Salas A; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
  • Heyn H; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
  • Martelotto LG; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
Genome Biol ; 25(1): 81, 2024 03 29.
Article in En | MEDLINE | ID: mdl-38553769
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: RNA / Genomics Limits: Animals / Humans Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: España Country of publication: Reino Unido
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: RNA / Genomics Limits: Animals / Humans Language: En Journal: Genome Biol Journal subject: BIOLOGIA MOLECULAR / GENETICA Year: 2024 Document type: Article Affiliation country: España Country of publication: Reino Unido