Research Progress in Single-Cell RNA-Seq of Plant

doi:10.13560/j.cnki.biotech.bull.1985.2020-1011

Abstract

Abstract:

Single-cell RNA-Seq（scRNA-seq）is a technology to analyze gene expression at single cell level. Currently PCR plate-based and droplet-based protocols are 2 major popular ones used in the studies of plant. Here,we firstly outline the technical principles and data analysis procedure of plant scRNA-seq,and then introduce its research status,focusing on how scRNA-seq can be used to detect distinct plant cell types,to reveal cell evolution trajectories and to construct inter-cell regulatory networks. ScRNA-seq may provide a new perspective on plant research,and help to understand and identify critical cellular biological processes in complex tissues.

Key words: single cell, RNA-sequencing, droplet-based protocol, PCR plate-based protocol, cell-type-specific

LI Yi, SUN Chao. Research Progress in Single-Cell RNA-Seq of Plant[J]. Biotechnology Bulletin, 2021, 37(1): 60-66.

Figures/Tables 3

References 57

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建库方法	分析技术	捕获细胞数目	扩增技术	转录本覆盖率	参考文献
多孔板法	Smartseq2	94-384/plate	PCR	全长	[10]
	CEL-seq2	94-384/plate	IVT	3'端	[11]
液滴法	Chromium	80 000+	PCR	3'端	[13]
	Drop-seq	50 000+	PCR	3'端	[14]
	inDrop	40 000+	PCR	3'端	[15]

建库方法	分析技术	捕获细胞数目	扩增技术	转录本覆盖率	参考文献
多孔板法	Smartseq2	94-384/plate	PCR	全长	[10]
	CEL-seq2	94-384/plate	IVT	3'端	[11]
液滴法	Chromium	80 000+	PCR	3'端	[13]
	Drop-seq	50 000+	PCR	3'端	[14]
	inDrop	40 000+	PCR	3'端	[15]

建库方法	分析技术	物种	样本类型	细胞数	总基因数（转录本数）	基因数（转录本数）/细胞	参考文献
多孔板法	Smart-seq2	拟南芥	根	238	——	——	[8]
	Cell-seq2	玉米	生殖细胞	144	101 245*	——	[9]
	Cell-seq2	拟南芥	静止中心细胞	24	——	14 000	[53]
			中柱细胞	7	——	4 312	[53]
液滴法	Chromium	拟南芥	根（3个生物学重复）	7 522	>22 000	5 000	[16]
	Chromium	拟南芥	根（2个生物学重复）	4 727	16 975	4 276	[17]
	Chromium	拟南芥	根	3 121	22 419	2 445	[18]
			根（热胁迫）	1 009	21 237	1 009	[18]
			根	1 079	22 971	4 079	[18]
	Chromium	拟南芥	根	7 695	23 161	——	[19]
	Chromium	拟南芥	子叶	12 844	——	——	[20]
	Drop-seq	拟南芥	根	6 102	——	>1 000*	[54]
			根（1%蔗糖处理）	6 096	——	——	[54]
	Drop-seq	拟南芥	根	374	——	——	[55]

建库方法	分析技术	物种	样本类型	细胞数	总基因数（转录本数）	基因数（转录本数）/细胞	参考文献
多孔板法	Smart-seq2	拟南芥	根	238	——	——	[8]
	Cell-seq2	玉米	生殖细胞	144	101 245*	——	[9]
	Cell-seq2	拟南芥	静止中心细胞	24	——	14 000	[53]
			中柱细胞	7	——	4 312	[53]
液滴法	Chromium	拟南芥	根（3个生物学重复）	7 522	>22 000	5 000	[16]
	Chromium	拟南芥	根（2个生物学重复）	4 727	16 975	4 276	[17]
	Chromium	拟南芥	根	3 121	22 419	2 445	[18]
			根（热胁迫）	1 009	21 237	1 009	[18]
			根	1 079	22 971	4 079	[18]
	Chromium	拟南芥	根	7 695	23 161	——	[19]
	Chromium	拟南芥	子叶	12 844	——	——	[20]
	Drop-seq	拟南芥	根	6 102	——	>1 000*	[54]
			根（1%蔗糖处理）	6 096	——	——	[54]
	Drop-seq	拟南芥	根	374	——	——	[55]