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Single-nuclei RNA-sequencing of plant tissues using a nanowell-based system

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Item Type:Article
Title:Single-nuclei RNA-sequencing of plant tissues using a nanowell-based system
Creators Name:Sunaga-Franze, D. and Muino, J.M. and Braeuning, C. and Xu, X. and Zong, M. and Smaczniak, C. and Yan, W. and Fischer, C. and Vidal, R. and Kliem, M. and Kaufmann, K. and Sauer, S.
Abstract:Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nuclei isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nuclei isolation method by using different plant materials from different species. The potential of our snRNA-seq method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process and predicted potential target genes of these transcription factors. Our nuclei isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
Keywords:Arabidopsis Thaliana Seedlings, Single-Nuclei Isolation, Anther, Flower Development, SnRNA-Seq
Source:Plant Journal
ISSN:0960-7412
Publisher:Wiley-Blackwell
Volume:108
Number:3
Page Range:859-869
Date:5 November 2021
Official Publication:https://doi.org/10.1111/tpj.15458
PubMed:View item in PubMed

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