Plant Nuclei Isolation for Single-Nucleus RNA Sequencing

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 2686; p. 307
• Main Authors: Xin, Xu, Du, Fei, Jiao, Yuling
• Format: Journal Article
• Language: English
• Published: United States 2023
• Subjects: Plant; Nuclei; Shoot apices; snRNA-seq
• ISSN: 1940-6029
• DOI: 10.1007/978-1-0716-3299-4_15

Transcriptome profiling has been significantly hampered by the heterogeneity among individual cells within a tissue or an organ. Recent advances in single cell transcriptome profiling have significantly advanced our understanding of the transcriptome. However, plant single-cell RNA sequencing (scRNA-seq) relies on the isolation of protoplasts, which is not only impossible for many cell types but also induces acute wounding responses. To solve these problems, single-nucleus RNA sequencing (snRNA-seq) has been applied to plant research, in which nuclei are isolated and subject to encapsulation and profiling. Compared with scRNA-seq, snRNA-seq can be applied to a wider range of tissue types and plant species. Nevertheless, fewer transcripts can be obtained from each nucleus than each protoplast. In this chapter, we describe a detailed and general protocol to prepare nuclei from plant tissues that are ready for subsequent library construction and high-throughput sequencing.