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RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Jun Komatsu, Alba Cico, Raya Poncin, Maël Le Bohec, Jörg Morf, Stanislav Lipin, Antoine Graindorge, Hélène Eckert, Azadeh Saffarian, Léa Cathaly, Frédéric Guérin, Sara Majello, Damien Ulveling, Anaïs Vayaboury, Nicolas Fernandez, Dilyana Dimitrova, Xavier Bussell, Yannick Fourne, Pierre Chaumat, Barbara André, Elodie Baldivia, Ulysse Godet, Mathieu Guinin, Vivien Moretto, Joy Ismail, Olivier Caille, Natacha Roblot, Carine Beaupère, Alexandrine Liboz, Ghislaine Guillemain, Bertrand Blondeau, Pierre Walrafen, View ORCID ProfileStuart Edelstein
doi: https://doi.org/10.1101/2022.07.01.498266
Jun Komatsu
1Scipio bioscience, Paris, France
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Alba Cico
1Scipio bioscience, Paris, France
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Raya Poncin
1Scipio bioscience, Paris, France
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Maël Le Bohec
1Scipio bioscience, Paris, France
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Jörg Morf
1Scipio bioscience, Paris, France
3Skyhawk Therapeutics, Basel, Switzerland
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Stanislav Lipin
1Scipio bioscience, Paris, France
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Antoine Graindorge
1Scipio bioscience, Paris, France
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Hélène Eckert
1Scipio bioscience, Paris, France
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Azadeh Saffarian
1Scipio bioscience, Paris, France
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Léa Cathaly
1Scipio bioscience, Paris, France
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Frédéric Guérin
1Scipio bioscience, Paris, France
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Sara Majello
1Scipio bioscience, Paris, France
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Damien Ulveling
1Scipio bioscience, Paris, France
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Anaïs Vayaboury
1Scipio bioscience, Paris, France
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Nicolas Fernandez
1Scipio bioscience, Paris, France
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Dilyana Dimitrova
1Scipio bioscience, Paris, France
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Xavier Bussell
1Scipio bioscience, Paris, France
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Yannick Fourne
1Scipio bioscience, Paris, France
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Pierre Chaumat
1Scipio bioscience, Paris, France
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Barbara André
1Scipio bioscience, Paris, France
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Elodie Baldivia
1Scipio bioscience, Paris, France
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Ulysse Godet
1Scipio bioscience, Paris, France
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Mathieu Guinin
1Scipio bioscience, Paris, France
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Vivien Moretto
1Scipio bioscience, Paris, France
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Joy Ismail
1Scipio bioscience, Paris, France
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Olivier Caille
1Scipio bioscience, Paris, France
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Natacha Roblot
2Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012 Paris, France
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Carine Beaupère
2Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012 Paris, France
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Alexandrine Liboz
2Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012 Paris, France
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Ghislaine Guillemain
2Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012 Paris, France
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Bertrand Blondeau
2Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, F-75012 Paris, France
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Pierre Walrafen
1Scipio bioscience, Paris, France
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  • For correspondence: pierre.walrafen@scipio.bio stuart.edelstein@scipio.bio
Stuart Edelstein
1Scipio bioscience, Paris, France
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  • ORCID record for Stuart Edelstein
  • For correspondence: pierre.walrafen@scipio.bio stuart.edelstein@scipio.bio
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ABSTRACT

Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead—cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.

Competing Interest Statement

Authors are employed by Scipio bioscience founded by corresponding authors Pierre Walrafen and Stuart Edelstein, except authors from St. Antoine Hospital who have no competing interests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 02, 2022.
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RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding
Jun Komatsu, Alba Cico, Raya Poncin, Maël Le Bohec, Jörg Morf, Stanislav Lipin, Antoine Graindorge, Hélène Eckert, Azadeh Saffarian, Léa Cathaly, Frédéric Guérin, Sara Majello, Damien Ulveling, Anaïs Vayaboury, Nicolas Fernandez, Dilyana Dimitrova, Xavier Bussell, Yannick Fourne, Pierre Chaumat, Barbara André, Elodie Baldivia, Ulysse Godet, Mathieu Guinin, Vivien Moretto, Joy Ismail, Olivier Caille, Natacha Roblot, Carine Beaupère, Alexandrine Liboz, Ghislaine Guillemain, Bertrand Blondeau, Pierre Walrafen, Stuart Edelstein
bioRxiv 2022.07.01.498266; doi: https://doi.org/10.1101/2022.07.01.498266
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RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding
Jun Komatsu, Alba Cico, Raya Poncin, Maël Le Bohec, Jörg Morf, Stanislav Lipin, Antoine Graindorge, Hélène Eckert, Azadeh Saffarian, Léa Cathaly, Frédéric Guérin, Sara Majello, Damien Ulveling, Anaïs Vayaboury, Nicolas Fernandez, Dilyana Dimitrova, Xavier Bussell, Yannick Fourne, Pierre Chaumat, Barbara André, Elodie Baldivia, Ulysse Godet, Mathieu Guinin, Vivien Moretto, Joy Ismail, Olivier Caille, Natacha Roblot, Carine Beaupère, Alexandrine Liboz, Ghislaine Guillemain, Bertrand Blondeau, Pierre Walrafen, Stuart Edelstein
bioRxiv 2022.07.01.498266; doi: https://doi.org/10.1101/2022.07.01.498266

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