Accession PRJCA001393
Title A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root
Relevance Agricultural
Data types Transcriptome or Gene expression
Organisms Arabidopsis thaliana
Description Cells have the inherent heterogeneity. Recent advances in the single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations. Using high-throughput single-cell RNA sequencing (scRNA-seq) assay, we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes. A total of 24 putative cell clusters and their cluster-specific marker genes were identified. The spatial distribution and temporal ordering of the individual cell at different developmental stages illustrate their hierarchical structure and reconstructs continuous differentiation trajectory of root development. Moreover, we found that each root cell cluster exhibits distinct patterns in ion assimilation and hormone response. Our study thus reveals high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at the single-cell resolution. We have implemented a supplementary web server ( to facilitate the use of the datasets generated in this study.
Sample scope Single cell
Release date 2019-05-06
PubMed ID Article title Journal name DOI Year
Agency program Grant ID Grant title
State Key Basic Research Program of China 2013CB127000
National Natural Science Foundation of China (NSFC) 31430013
National Natural Science Foundation of China (NSFC) 31222029
National Natural Science Foundation of China (NSFC) 912173023
National Natural Science Foundation of China (NSFC) 31525004
Strategic Priority Research Program of the Chinese Academy of Sciences XDB27030101
Young Elite Scientists Sponsorship Program by CAST 2016QNRC001
National Postdoctoral Program for Innovative Talents BX201600178
Sanofi-SIBS 2017 Post-doctoral Fellowship NA
Submitter Zhougeng    Xu  (
Organization Institute of Plant Physiology & Ecology, Chinese Academy of Sciences
Submission date 2019-04-26

Project Data

Resource name Description
BioSample (1) -
SAMC068470 Root Single-Cell RNA Sequencing
GSA (1) -
CRA001559 scRNA-seq-of-arabidopsis-root