FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

Laura Jiménez-Gracia; Doménica Marchese; Juan Camilo Nieto; Ginevra Caratù; Elisa Melón-Ardanaz; Victòria 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 C Rosenstiel; Eduard Batlle; Lisa M. Butler; Ian A. Parish; Jasmine Plummer; Ivo Glynne Gut; Azucena Salas; Holger Heyn; Luciano Gastón Martelotto

doi:10.1186/s13059-024-03219-5

BioinformaticsGenome biologyMar 29, 2024

Peer-reviewed journal article

FixNCut: Single-cell genomics through reversible tissue fixation and dissociation

Laura Jiménez-Gracia iD, Doménica Marchese iD, Juan Camilo Nieto iD, Ginevra Caratù iD, Elisa Melón-Ardanaz iD, Victòria Gudiño iD, Sara Roth iD, Kellie Wise iD, Natalie K. Ryan, Kirk B. Jensen iD, Xavier Hernando‐Momblona iD, Joana P. Bernardes iD, Florian Tran iD, Laura Katharina Sievers iD, Stefan Schreiber iD, Maarten van den Berge iD, Tessa Kole iD, Petra L. van der Velde, Martijn C. Nawijn iD, Philip C Rosenstiel iD, Eduard Batlle iD, Lisa M. Butler iD, Ian A. Parish iD, Jasmine Plummer iD, Ivo Glynne Gut iD, , Luciano Gastón Martelotto iD

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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