ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Helena García-Castro; Nathan J. Kenny; Marta Iglesias; Patricia Álvarez-Campos; Vincent Mason; Anamaria Elek; Anna Schönauer; Victoria A. Sleight; Jakke Neiro; Aziz Aboobaker; Jon Permanyer; Manuel Irimia; Arnau Sebé-Pedrós; Jordi Solana

doi:10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez-Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana^*

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

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

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Abstract

Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable. As a proof of principle, we provide single-cell transcriptomic data of different species, using both droplet-based and combinatorial barcoding single-cell methods. ACME uses affordable reagents, can be done in most laboratories and even in the field, and thus will accelerate our knowledge of cell types across the tree of life.

Original language	English
Article number	89
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02302-5
Publication status	Published - 8 Apr 2021

Bibliographical note

Funding Information:
We thank Helen Ferry and Liam Hardy at the Experimental Medicine Division Flow Cytometry Facility at the Nuffield Department of Clinical Medicine (University of Oxford), Michal Maj at the Flow Cytometry Facility at the Dunn School of Pathology (University of Oxford), and Òscar Fornas at the Centre for Genomic Regulation/Universitat Pompeu Fabra FACS Unit (Barcelona) for their help and advice with flow cytometry. We thank Zhong Yap from the Aboobaker Lab at Oxford University for the help with irradiation. We thank Alistair McGregor at Oxford Brookes University for providing useful comments and discussion about the dissociation; Teresa Adell of the Department of Genetics, University of Barcelona; Markus Grohme at MPI-CBG (Dresden); and Christopher Laumer at the European Bioinformatics Institute (Cambridge) for the discussion, advice on the protocol, and comments on the manuscript. We thank Mireya Plass at the Centre for Regenerative Medicine of Barcelona for the computational analysis advice and for the critical review of the manuscript. The review history is available as Additional file 6. Barbara Cheifet was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Funding Information:
This work was supported by an MRC grant (MR/S007849/1) and a Royal Society Grant (RGS\R1\191278) to JS. HG-C was supported by a Nigel Groome studentship from Oxford Brookes University. PA-C was supported by an EMBO Long Term Fellowship (ALTF-217-2018). JN was supported by funding from a BBSRC grant (BB/M011224/1) and the Osk. Huttunen Foundation (Doctoral grant).

Publisher Copyright:
© 2021, The Author(s).

Keywords

Combinatorial indexing
Dissociation
Fixation
Planarian
RNA-seq
Single-cell transcriptomics
SPLiT-seq

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10.1186/s13059-021-02302-5

Garcia-Castro_etal_GB_ACME_Dissociation_A_VOR
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García-Castro, H., Kenny, N. J., Iglesias, M., Álvarez-Campos, P., Mason, V., Elek, A., Schönauer, A., Sleight, V. A., Neiro, J., Aboobaker, A., Permanyer, J., Irimia, M., Sebé-Pedrós, A., & Solana, J. (2021). ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biology, 22(1), Article 89. https://doi.org/10.1186/s13059-021-02302-5

García-Castro, H, Kenny, NJ, Iglesias, M, Álvarez-Campos, P, Mason, V, Elek, A, Schönauer, A, Sleight, VA, Neiro, J, Aboobaker, A, Permanyer, J, Irimia, M, Sebé-Pedrós, A & Solana, J 2021, 'ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics', Genome Biology, vol. 22, no. 1, 89. https://doi.org/10.1186/s13059-021-02302-5

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abstract = "Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable. As a proof of principle, we provide single-cell transcriptomic data of different species, using both droplet-based and combinatorial barcoding single-cell methods. ACME uses affordable reagents, can be done in most laboratories and even in the field, and thus will accelerate our knowledge of cell types across the tree of life.",

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AU - Mason, Vincent

AU - Elek, Anamaria

AU - Schönauer, Anna

AU - Sleight, Victoria A.

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AU - Aboobaker, Aziz

AU - Permanyer, Jon

AU - Irimia, Manuel

AU - Sebé-Pedrós, Arnau

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ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Abstract

Bibliographical note

Keywords

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