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

• Published in: Scientific reports Vol. 13; no. 1; p. 4866
• Main Authors: Komatsu, Jun, Cico, Alba, Poncin, Raya, Le Bohec, Maël, Morf, Jörg, Lipin, Stanislav, Graindorge, Antoine, Eckert, Hélène, Saffarian, Azadeh, Cathaly, Léa, Guérin, Frédéric, Majello, Sara, Ulveling, Damien, Vayaboury, Anaïs, Fernandez, Nicolas, Dimitrova, Dilyana, Bussell, Xavier, Fourne, Yannick, Chaumat, Pierre, André, Barbara, Baldivia, Elodie, Godet, Ulysse, Guinin, Mathieu, Moretto, Vivien, Ismail, Joy, Caille, Olivier, Roblot, Natacha, Beaupère, Carine, Liboz, Alexandrine, Guillemain, Ghislaine, Blondeau, Bertrand, Walrafen, Pierre, Edelstein, Stuart
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.03.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/1647; 631/337; 631/80; Animals; Cardiomyocytes; Complementary DNA; Experimental design; Freezing; Gelation; Gene expression; Gene Expression Profiling; Humanities and Social Sciences; Humans; Hydrogels; Hydrogels - chemistry; Islet cells; Life Sciences; Lysis; Mice; Microfluidics; multidisciplinary; Peripheral blood mononuclear cells; Reverse transcription; Sample preparation; Science; Science (multidisciplinary); Sequence Analysis, RNA - methods; Single-Cell Analysis - methods
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-31915-y

Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets. Cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcoded beads for further processing with reverse transcription and preparation for cDNA sequencing. As a proof of concept, analysis of PBMC using RevGel-seq achieves results similar to microfluidic-based technologies when using the same original sample and the same data analysis software. In addition, a clinically relevant application of RevGel-seq is presented for pancreatic islet cells. Furthermore, characterizations carried out on cardiomyocytes demonstrate that the hydrogel technology readily accommodates very large cells. Standard analyses are in the 10,000-input cell range with the current gelation device, in order to satisfy common requirements for single-cell research. A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.