Single-Cell RNA Sequencing for Plant Research: Insights and Possible Benefits

Single‐cell RNA‐sequencing of Nicotiana attenuata corolla cells reveals the biosynthetic pathway of a floral scent

(2022) Moonyoung Kang et al.   NEW PHYTOLOGIST

Identification of the Regulators of Epidermis Development under Drought- and Salt-Stressed Conditions by Single-Cell RNA-Seq

(2022) Zhixin Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An Efficient and Universal Protoplast Isolation Protocol Suitable for Transient Gene Expression Analysis and Single-Cell RNA Sequencing

(2022) Juanjuan Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of new marker genes from plant single‐cell RNA‐seq data using interpretable machine learning methods

(2022) Haidong Yan et al.   NEW PHYTOLOGIST

Identification of novel regulators required for early development of vein pattern in the cotyledons by single‐cell RNA ‐sequencing

(2022) Zhixin Liu et al.   PLANT JOURNAL

Single but not alone: the transcriptomes of 14 000 single cells from developing cotyledon veins

(2022) Leonie Verhage   PLANT JOURNAL

A conserved superlocus regulates above- and belowground root initiation

(2022) Moutasem Omary et al.   SCIENCE

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

(2021) Xiaosa Xu et al.   DEVELOPMENTAL CELL

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

(2021) Andrew Farmer et al.   Molecular Plant

Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience

(2021) Rajiv K. Tripathi et al.   PLANT CELL AND ENVIRONMENT

Advances and Opportunities of Single-Cell Transcriptomics for Plant Research

(2021) Carolin Seyfferth et al.   Annual Review of Plant Biology

A cis-regulatory atlas in maize at single-cell resolution

(2021) Alexandre P. Marand et al.   CELL

A new era for plant science: spatial single-cell transcriptomics

(2021) Stefania Giacomello   CURRENT OPINION IN PLANT BIOLOGY

Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf

(2021) Camila B. Lopez-Anido et al.   DEVELOPMENTAL CELL

Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root

(2021) Tian-Qi Zhang et al.   Nature Communications

Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities

(2021) Rachel Shahan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Single-cell transcriptome atlas of the leaf and root of rice seedlings

(2021) Yu Wang et al.   Journal of Genetics and Genomics

A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root

(2021) Moritz Graeff et al.   Molecular Plant

Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation

(2021) Laura Serrano-Ron et al.   Molecular Plant

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

(2021) Michael W. Dorrity et al.   Nature Communications

Single‐cell RNA sequencing profiles of stem‐differentiating xylem in poplar

(2021) Jianbo Xie et al.   PLANT BIOTECHNOLOGY JOURNAL

Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles

(2021) Federico Apelt et al.   PLANT PHYSIOLOGY

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

The promise of single-cell genomics in plants

(2020) José L McFaline-Figueroa et al.   CURRENT OPINION IN PLANT BIOLOGY

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing

(2020) Zhixin Liu et al.   Molecular Plant

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

(2020) Fabian Imdahl et al.   Nature Microbiology

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

(2020) Rahul Shaw et al.   Molecular Plant

Transcriptional landscape of rice roots at the single-cell resolution

(2020) Qing Liu et al.   Molecular Plant

Plant stem-cell organization and differentiation at single-cell resolution

(2020) James W. Satterlee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Kook Hui Ryu et al.   PLANT PHYSIOLOGY

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

(2019) Minoru Kubo et al.   NUCLEIC ACIDS RESEARCH

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

Towards Building a Plant Cell Atlas

(2019) Seung Y. Rhee et al.   TRENDS IN PLANT SCIENCE

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

(2019) Christine N. Shulse et al.   Cell Reports

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

(2019) Gina M. Turco et al.   Cell Reports

Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics

(2019) Charlotte Rich-Griffin et al.   TRENDS IN PLANT SCIENCE

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization

(2019) Chiara Baccin et al.   NATURE CELL BIOLOGY

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

(2017) Audrey P. Gasch et al.   PLOS BIOLOGY

Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions

(2016) Idan Efroni et al.   CELL

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi

(2015) Caroline Gutjahr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis

(2013) Y. Geng et al.   PLANT CELL

De Novo Assembly, Gene Annotation and Marker Development Using Illumina Paired-End Transcriptome Sequences in Celery (Apium graveolens L.)

(2013) Nan Fu et al.   PLoS One

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity

(2011) Massimo Iorizzo et al.   BMC GENOMICS

Cell Identity Regulators Link Development and Stress Responses in the Arabidopsis Root

(2011) Anjali S. Iyer-Pascuzzi et al.   DEVELOPMENTAL CELL

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

(2011) Hinako Takehisa et al.   PLANT JOURNAL

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress

(2008) J. R. Dinneny et al.   SCIENCE