Glyoxal as an alternative fixative for single-cell RNA sequencing

• Verfasst von: Bageritz, Josephine [VerfasserIn]
• Verfasst von: Krausse, Niklas [VerfasserIn]
• Verfasst von: Yousefian, Schayan [VerfasserIn]
• Verfasst von: Leible, Svenja [VerfasserIn]
• Verfasst von: Valentini, Erica [VerfasserIn]
• Verfasst von: Boutros, Michael [VerfasserIn]
• Titel: Glyoxal as an alternative fixative for single-cell RNA sequencing
• Verf.angabe: Josephine Bageritz, Niklas Krausse, Schayan Yousefian, Svenja Leible, Erica Valentini, Michael Boutros
• E-Jahr: 2023
• Jahr: October 2023
• Umfang: 7 S.
• Illustrationen: Illustrationen
• Fussnoten: Veröffentlicht: 26. Juli 2023 ; Gesehen am 06.06.2024
• Titel Quelle: Enthalten in: G3: Genes, genomes, genetics
• Ort Quelle: Pittsburgh, PA : Genetics Soc. of America, 2011
• Jahr Quelle: 2023
• Band/Heft Quelle: 13(2023), 10 vom: Okt., Artikel-ID jkad160, Seite 1-7
• ISSN Quelle: 2160-1836
• DOI: doi:10.1093/g3journal/jkad160
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 1890805556

Abstract

Single-cell RNA sequencing has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms, and understand the heterogeneity in cellular responses. Nevertheless, sample collection and processing remain a severe bottleneck for single-cell RNA sequencing experiments. Cell isolation protocols often lead to significant changes in the transcriptomes of cells, requiring novel methods to preserve cell states. Here, we developed and benchmarked protocols using glyoxal as a fixative for single-cell RNA sequencing applications. Using Drop-seq methodology, we detected a large number of transcripts and genes from glyoxal-fixed Drosophila cells after single-cell RNA sequencing. The effective glyoxal fixation of transcriptomes in Drosophila and human cells was further supported by a high correlation of gene expression data between glyoxal-fixed and unfixed samples. Accordingly, we also found highly expressed genes overlapping to a large extent between experimental conditions. These results indicated that our fixation protocol did not induce considerable changes in gene expression and conserved the transcriptome for subsequent single-cell isolation procedures. In conclusion, we present glyoxal as a suitable fixative for Drosophila cells and potentially cells of other species that allow high-quality single-cell RNA sequencing applications.