Single cell RNA-sequencing in Arabidopsis root tissues
(2023)
Plant gene regulatory networks : methods and protocols.
In Methods in Molecular Biology
2698.
p.41-56
- Author
- Yuji Ke (UGent) , Max Minne (UGent) , Thomas Eekhout (UGent) and Bert De Rybel (UGent)
- Organization
- Abstract
- Droplet-based single-cell RNA-sequencing (scRNA-seq) empowers transcriptomic profiling with an unprecedented resolution, facilitating insights into the cellular heterogeneity of tissues, developmental progressions, stress-response dynamics, and more at single-cell level. In this chapter, we describe the experimental workflow of processing Arabidopsis root tissue into protoplasts and generating single-cell transcriptomes. We also describe the general computational workflow of visualizing and utilizing scRNA-seq data. This protocol can be used as a starting point for establishing a scRNA-seq workflow.
- Keywords
- Arabidopsis, FACS, Protoplast, Root, Single cell, Transcriptomics, scRNA-seq
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Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HKW5EX1KKZXFGZ20HDGCA5NC
- MLA
- Ke, Yuji, et al. “Single Cell RNA-Sequencing in Arabidopsis Root Tissues.” Plant Gene Regulatory Networks : Methods and Protocols, edited by Kerstin Kaufmann and Klaas Vandepoele, vol. 2698, Humana, 2023, pp. 41–56, doi:10.1007/978-1-0716-3354-0_4.
- APA
- Ke, Y., Minne, M., Eekhout, T., & De Rybel, B. (2023). Single cell RNA-sequencing in Arabidopsis root tissues. In K. Kaufmann & K. Vandepoele (Eds.), Plant gene regulatory networks : methods and protocols (Vol. 2698, pp. 41–56). https://doi.org/10.1007/978-1-0716-3354-0_4
- Chicago author-date
- Ke, Yuji, Max Minne, Thomas Eekhout, and Bert De Rybel. 2023. “Single Cell RNA-Sequencing in Arabidopsis Root Tissues.” In Plant Gene Regulatory Networks : Methods and Protocols, edited by Kerstin Kaufmann and Klaas Vandepoele, 2698:41–56. New York, NY, USA: Humana. https://doi.org/10.1007/978-1-0716-3354-0_4.
- Chicago author-date (all authors)
- Ke, Yuji, Max Minne, Thomas Eekhout, and Bert De Rybel. 2023. “Single Cell RNA-Sequencing in Arabidopsis Root Tissues.” In Plant Gene Regulatory Networks : Methods and Protocols, ed by. Kerstin Kaufmann and Klaas Vandepoele, 2698:41–56. New York, NY, USA: Humana. doi:10.1007/978-1-0716-3354-0_4.
- Vancouver
- 1.Ke Y, Minne M, Eekhout T, De Rybel B. Single cell RNA-sequencing in Arabidopsis root tissues. In: Kaufmann K, Vandepoele K, editors. Plant gene regulatory networks : methods and protocols. New York, NY, USA: Humana; 2023. p. 41–56.
- IEEE
- [1]Y. Ke, M. Minne, T. Eekhout, and B. De Rybel, “Single cell RNA-sequencing in Arabidopsis root tissues,” in Plant gene regulatory networks : methods and protocols, vol. 2698, K. Kaufmann and K. Vandepoele, Eds. New York, NY, USA: Humana, 2023, pp. 41–56.
@incollection{01HKW5EX1KKZXFGZ20HDGCA5NC,
abstract = {{Droplet-based single-cell RNA-sequencing (scRNA-seq) empowers transcriptomic profiling with an unprecedented resolution, facilitating insights into the cellular heterogeneity of tissues, developmental progressions, stress-response dynamics, and more at single-cell level. In this chapter, we describe the experimental workflow of processing Arabidopsis root tissue into protoplasts and generating single-cell transcriptomes. We also describe the general computational workflow of visualizing and utilizing scRNA-seq data. This protocol can be used as a starting point for establishing a scRNA-seq workflow.}},
author = {{Ke, Yuji and Minne, Max and Eekhout, Thomas and De Rybel, Bert}},
booktitle = {{Plant gene regulatory networks : methods and protocols}},
editor = {{Kaufmann, Kerstin and Vandepoele, Klaas}},
isbn = {{9781071633533}},
issn = {{1064-3745}},
keywords = {{Arabidopsis,FACS,Protoplast,Root,Single cell,Transcriptomics,scRNA-seq}},
language = {{eng}},
pages = {{41--56}},
publisher = {{Humana}},
series = {{Methods in Molecular Biology}},
title = {{Single cell RNA-sequencing in Arabidopsis root tissues}},
url = {{http://doi.org/10.1007/978-1-0716-3354-0_4}},
volume = {{2698}},
year = {{2023}},
}
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