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

doi:10.1186/s13059-024-03219-5

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 RosenstielEduard Batlle, Lisa M Butler, Ian A Parish, Jasmine Plummer, Ivo Gut, Azucena Salas, Holger Heyn^*, Luciano G Martelotto^*

^*Corresponding author for this work

Groningen Research Institute for Asthma and COPD (GRIAC)

Research output: Contribution to journal › Article › Academic › peer-review

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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.

Original language	English
Article number	81
Number of pages	36
Journal	Genome Biology
Volume	25
DOIs	https://doi.org/10.1186/s13059-024-03219-5
Publication status	Published - 29-Mar-2024

Keywords

Humans
Animals
Mice
Tissue Fixation/methods
Reproducibility of Results
Sequence Analysis, RNA/methods
RNA/genetics
Genomics/methods
Single-Cell Analysis/methods

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FixNCutFinal publisher's version, 6 MBLicence: CC BY

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Jiménez-Gracia, L., Marchese, D., Nieto, J. C., Caratù, G., Melón-Ardanaz, E., Gudiño, V., Roth, S., Wise, K., Ryan, N. K., Jensen, K. B., Hernando-Momblona, X., Bernardes, J. P., Tran, F., Sievers, L. K., Schreiber, S., van den Berge, M., Kole, T., van der Velde, P. L., Nawijn, M. C., ... Martelotto, L. G. (2024). FixNCut: single-cell genomics through reversible tissue fixation and dissociation. Genome Biology, 25, Article 81. https://doi.org/10.1186/s13059-024-03219-5

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title = "FixNCut: single-cell genomics through reversible tissue fixation and dissociation",

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 = "Humans, Animals, Mice, Tissue Fixation/methods, Reproducibility of Results, Sequence Analysis, RNA/methods, RNA/genetics, Genomics/methods, Single-Cell Analysis/methods",

author = "Laura Jim{\'e}nez-Gracia and Domenica Marchese and Nieto, {Juan C} and Ginevra Carat{\`u} and Elisa Mel{\'o}n-Ardanaz and Victoria Gudi{\~n}o and Sara Roth and Kellie Wise and Ryan, {Natalie K} and Jensen, {Kirk B} and Xavier Hernando-Momblona and Bernardes, {Joana P} and Florian Tran and Sievers, {Laura Katharina} and Stefan Schreiber and {van den Berge}, Maarten and Tessa Kole and {van der Velde}, {Petra L} and Nawijn, {Martijn C} and Philip Rosenstiel and Eduard Batlle and Butler, {Lisa M} and Parish, {Ian A} and Jasmine Plummer and Ivo Gut and Azucena Salas and Holger Heyn and Martelotto, {Luciano G}",

note = "{\textcopyright} 2024. Crown.",

year = "2024",

month = mar,

day = "29",

doi = "10.1186/s13059-024-03219-5",

language = "English",

volume = "25",

journal = "Genome Biology",

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Jiménez-Gracia, L, Marchese, D, Nieto, JC, Caratù, G, Melón-Ardanaz, E, Gudiño, V, Roth, S, Wise, K, Ryan, NK, Jensen, KB, Hernando-Momblona, X, Bernardes, JP, Tran, F, Sievers, LK, Schreiber, S, van den Berge, M, Kole, T, van der Velde, PL , Nawijn, MC, Rosenstiel, P, Batlle, E, Butler, LM, Parish, IA, Plummer, J, Gut, I, Salas, A, Heyn, H & Martelotto, LG 2024, 'FixNCut: single-cell genomics through reversible tissue fixation and dissociation', Genome Biology, vol. 25, 81. https://doi.org/10.1186/s13059-024-03219-5

TY - JOUR

T1 - FixNCut

T2 - single-cell genomics through reversible tissue fixation and dissociation

AU - Jiménez-Gracia, Laura

AU - Marchese, Domenica

AU - Nieto, Juan C

AU - Caratù, Ginevra

AU - Melón-Ardanaz, Elisa

AU - Gudiño, Victoria

AU - Roth, Sara

AU - Wise, Kellie

AU - Ryan, Natalie K

AU - Jensen, Kirk B

AU - Hernando-Momblona, Xavier

AU - Bernardes, Joana P

AU - Tran, Florian

AU - Sievers, Laura Katharina

AU - Schreiber, Stefan

AU - van den Berge, Maarten

AU - Kole, Tessa

AU - van der Velde, Petra L

AU - Nawijn, Martijn C

AU - Rosenstiel, Philip

AU - Batlle, Eduard

AU - Butler, Lisa M

AU - Parish, Ian A

AU - Plummer, Jasmine

AU - Gut, Ivo

AU - Salas, Azucena

AU - Heyn, Holger

AU - Martelotto, Luciano G

PY - 2024/3/29

Y1 - 2024/3/29

N2 - 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.

AB - 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.

KW - Humans

KW - Animals

KW - Mice

KW - Tissue Fixation/methods

KW - Reproducibility of Results

KW - Sequence Analysis, RNA/methods

KW - RNA/genetics

KW - Genomics/methods

KW - Single-Cell Analysis/methods

U2 - 10.1186/s13059-024-03219-5

DO - 10.1186/s13059-024-03219-5

M3 - Article

C2 - 38553769

SN - 1465-6906

VL - 25

JO - Genome Biology

JF - Genome Biology

M1 - 81

ER -

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

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Keywords

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