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Title: High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

Abstract

Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1547226
Alternate Identifier(s):
OSTI ID: 1623647
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Cell Reports
Additional Journal Information:
Journal Name: Cell Reports Journal Volume: 27 Journal Issue: 7; Journal ID: ISSN 2211-1247
Publisher:
Elsevier
Country of Publication:
Netherlands
Language:
English
Subject:
Cell Biology

Citation Formats

Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., and Dickel, Diane E. High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types. Netherlands: N. p., 2019. Web. doi:10.1016/j.celrep.2019.04.054.
Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., & Dickel, Diane E. High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types. Netherlands. doi:10.1016/j.celrep.2019.04.054.
Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., and Dickel, Diane E. Wed . "High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types". Netherlands. doi:10.1016/j.celrep.2019.04.054.
@article{osti_1547226,
title = {High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types},
author = {Shulse, Christine N. and Cole, Benjamin J. and Ciobanu, Doina and Lin, Junyan and Yoshinaga, Yuko and Gouran, Mona and Turco, Gina M. and Zhu, Yiwen and O’Malley, Ronan C. and Brady, Siobhan M. and Dickel, Diane E.},
abstractNote = {Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.},
doi = {10.1016/j.celrep.2019.04.054},
journal = {Cell Reports},
number = 7,
volume = 27,
place = {Netherlands},
year = {2019},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1016/j.celrep.2019.04.054

Citation Metrics:
Cited by: 22 works
Citation information provided by
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