Advances and applications of single‐cell omics technologies in plant research

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

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

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 single-cell analysis of the Arabidopsis vegetative shoot apex

(2021) Tian-Qi Zhang et al.   DEVELOPMENTAL CELL

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 CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

(2021) Steven J. Wu et al.   NATURE BIOTECHNOLOGY

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

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

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

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

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

Stochastic gene expression drives mesophyll protoplast regeneration

(2021) Mengxue Xu et al.   Science Advances

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Profiling plant histone modification at single‐cell resolution using snCUT&Tag

(2021) Weizhi Ouyang et al.   PLANT BIOTECHNOLOGY JOURNAL

Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization

(2021) Pawel Roszak et al.   SCIENCE

Mass-spectrometry-based draft of the Arabidopsis proteome

(2020) Julia Mergner et al.   NATURE

Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

(2020) Yanpeng Xi et al.   PLANT JOURNAL

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication

(2020) Yixuan Kou et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Zhixin Liu 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

BRIF-seq: bisulfite-converted randomly integrated fragments sequencing at single cell level

(2019) Xiang Li et al.   Molecular Plant

Single gametophyte sequencing reveals that crossover events differ between sexes in maize

(2019) Cheng Luo et al.   Nature Communications

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

(2019) Craig L. Bohrson et al.   NATURE GENETICS

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

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

High-Throughput Single-Cell Sequencing with Linear Amplification

(2019) Yi Yin et al.   MOLECULAR CELL

Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants

(2019) Dongqing Shi et al.   GENOME RESEARCH

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

(2018) Daniel D Seaton et al.   Molecular Systems Biology

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Robust single-cell DNA methylome profiling with snmC-seq2

(2018) Chongyuan Luo et al.   Nature Communications

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

(2017) Xiao Dong et al.   NATURE METHODS

Scalable whole-genome single-cell library preparation without preamplification

(2017) Hans Zahn et al.   NATURE METHODS

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing

(2017) James Cooper et al.   Nature Protocols

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis )

(2017) Taotao Wang et al.   PLANT JOURNAL

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

(2017) Chongyi Chen et al.   SCIENCE

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Single nucleus sequencing reveals spermatid chromosome fragmentation as a possible cause of maize haploid induction

(2017) Xiang Li et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

Sequencing of Single Pollen Nuclei Reveals Meiotic Recombination Events at Megabase Resolution and Circumvents Segregation Distortion Caused by Postmeiotic Processes

(2017) Steven Dreissig et al.   Frontiers in Plant Science

Single-Cell (Multi)omics Technologies

(2016) Lia Chappell et al.   Annual Review of Genomics and Human Genetics

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

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

Review: imaging technologies for flow cytometry

(2016) Yuanyuan Han et al.   LAB ON A CHIP

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Integration of omic networks in a developmental atlas of maize

(2016) J. W. Walley et al.   SCIENCE

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

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

(2015) Evan Z. Macosko et al.   CELL

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

(2015) Junpeng Zhan et al.   PLANT CELL

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

(2015) Xiang Li et al.   Nature Communications

Calibrating genomic and allelic coverage bias in single-cell sequencing

(2015) Cheng-Zhong Zhang et al.   Nature Communications

Quantification of cell identity from single-cell gene expression profiles

(2015) Idan Efroni et al.   GENOME BIOLOGY

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

(2015) Yong Hou et al.   GigaScience

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Measuring Meiotic Crossovers via Multi-Locus Genotyping of Single Pollen Grains in Barley

(2015) Steven Dreissig et al.   PLoS One

Modeling genome coverage in single-cell sequencing

(2014) Timothy Daley et al.   BIOINFORMATICS

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Correlation of mRNA and protein abundance in the developing maize leaf

(2014) Lalit Ponnala et al.   PLANT JOURNAL

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

The protein expression landscape of the Arabidopsis root

(2012) J. J. Petricka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Cell-to-Cell Variability--A New Era in Molecular Biology

(2012) L. Pelkmans   SCIENCE

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics