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Single-cell RNA sequencing resolves molecular relationships among individual plant cells

Kook Hui Ryu, Ling Huang, Hyun Min Kang, John Schiefelbein
Kook Hui Ryu
University of Michigan CITY: Ann Arbor STATE: MI United States Of America [US]
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Ling Huang
University of Michigan CITY: Ann Arbor STATE: Michigan United States Of America [US]
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Hyun Min Kang
University of Michigan CITY: Ann Arbor STATE: MI United States Of America [US]
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John Schiefelbein
University of Michigan CITY: Ann Arbor STATE: Michigan POSTAL_CODE: 48109-1048 United States Of America [US]
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  • For correspondence: schiefel@umich.edu

Published February 2019. DOI: https://doi.org/10.1104/pp.18.01482

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  • {copyright, serif} 2019 American Society of Plant Biologists. All rights reserved.

Abstract

Single-cell RNA sequencing (scRNA-seq) has been used extensively to study cell-specific gene expression in animals, but it has not been widely applied to plants. Here, we describe the use of a commercially available droplet-based microfluidics platform for high-throughput scRNA-seq to obtain single-cell transcriptomes from protoplasts from more than 10,000 Arabidopsis root cells. We find that all major tissues and developmental stages are represented in this single-cell transcriptome population. Further, distinct sub-populations and rare cell types, including putative quiescent center (QC) cells, were identified. A focused analysis of root epidermal cell transcriptomes defined developmental trajectories for individual cells progressing from meristematic through mature stages of root-hair and non-hair cell differentiation. In addition, single-cell transcriptomes were obtained from root epidermis mutants, enabling a comparative analysis of gene expression at single-cell resolution and providing an unprecedented view of the impact of the mutated genes. Overall, this study demonstrates the feasibility and utility of scRNA-seq in plants and provides a first-generation gene expression map of the Arabidopsis root at single-cell resolution.

  • Received November 28, 2018.
  • Accepted January 29, 2019.

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Single-cell RNA sequencing in plants
Kook Hui Ryu, Ling Huang, Hyun Min Kang, John Schiefelbein
Plant Physiology Feb 2019, pp.01482.2018; DOI: 10.1104/pp.18.01482

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Single-cell RNA sequencing in plants
Kook Hui Ryu, Ling Huang, Hyun Min Kang, John Schiefelbein
Plant Physiology Feb 2019, pp.01482.2018; DOI: 10.1104/pp.18.01482
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Plant Physiology: 179 (2)
Plant Physiology
Vol. 179, Issue 2
Feb 2019
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