Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape

ScRNA-seq and ST-seq in liver research

(2023) Jia He et al.   Cell Regeneration

Methods and applications for single-cell and spatial multi-omics

(2023) Katy Vandereyken et al.   NATURE REVIEWS GENETICS

Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus

(2023) Xiehai Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

(2022) Rachel Shahan et al.   DEVELOPMENTAL CELL

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

(2022) Moonyoung Kang et al.   NEW PHYTOLOGIST

Transcriptional regulatory network of plant cold-stress responses

(2022) Satoshi Kidokoro et al.   TRENDS IN PLANT SCIENCE

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

(2022) Chang Liu et al.   DEVELOPMENTAL CELL

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

(2022) Mingyue Wang et al.   DEVELOPMENTAL CELL

The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves

(2022) Keke Xia et al.   DEVELOPMENTAL CELL

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

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

(2022) George Bawa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

(2022) Bin Li et al.   NATURE METHODS

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

(2022) Yajin Mo et al.   PLANT JOURNAL

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

Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the peg

(2022) Yiyang Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Single‐Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma

(2022) Zhihua Ou et al.   Advanced Science

PIN1 regulates epidermal cells development under drought and salt stress using single-cell analysis

(2022) George Bawa et al.   Frontiers in Plant Science

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

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

(2021) Kristen R. Maynard et al.   NATURE NEUROSCIENCE

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

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

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

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

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics

(2021) Chen Shengquan et al.   BIOINFORMATICS

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

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

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

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

Selected In Situ Hybridization Methods: Principles and Application

(2021) Dominika Veselinyová et al.   MOLECULES

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

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

(2021) Paul Datlinger et al.   NATURE METHODS

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

(2021) Sophia K. Longo et al.   NATURE REVIEWS GENETICS

Plant Single-Cell Multiomics: Cracking the Molecular Profiles of Plant Cells

(2021) Sandra Thibivilliers et al.   TRENDS IN PLANT SCIENCE

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

Tissue-specific transcriptomics reveal functional differences in floral development

(2021) Hailong Yang et al.   PLANT PHYSIOLOGY

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

(2021) Pawel Roszak et al.   SCIENCE

Crafting a blueprint for single-cell RNA sequencing

(2021) Tom Denyer et al.   TRENDS IN PLANT SCIENCE

High-throughput single-cell RNA sequencing

(2021) Tom Denyer et al.   TRENDS IN PLANT SCIENCE

Efficient and precise single-cell reference atlas mapping with Symphony

(2021) Joyce B. Kang et al.   Nature Communications

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

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

(2020) Zhixin Liu et al.   Molecular Plant

Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants

(2020) Cheng Luo et al.   TRENDS IN PLANT SCIENCE

Single-cell multiomics: technologies and data analysis methods

(2020) Jeongwoo Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

SpaGE: Spatial Gene Enhancement using scRNA-seq

(2020) Tamim Abdelaal et al.   NUCLEIC ACIDS RESEARCH

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

(2020) Jos R. Wendrich et al.   SCIENCE

Looking for Root Hairs to Overcome Poor Soils

(2020) Thanyakorn Rongsawat et al.   TRENDS IN PLANT SCIENCE

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

(2020) Alma Andersson et al.   Communications Biology

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Plant Single-Cell Metabolomics—Challenges and Perspectives

(2020) Leonardo Perez de Souza et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

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

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

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

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Molecular Mechanisms Driving Switch Behavior in Xylem Cell Differentiation

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

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

Spatially resolved transcriptomics reveals plant host responses to pathogens

(2019) Michael Giolai et al.   Plant Methods

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

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

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Estimates of incidence and mortality of cervical cancer in 2018: a worldwide analysis

(2019) Marc Arbyn et al.   Lancet Global Health

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

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

(2018) Alexander B. Rosenberg et al.   SCIENCE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Plant genetics: Spatial transcriptomics in plants

(2017) Liesbet Lieben   NATURE REVIEWS GENETICS

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

(2017) Sanjay M. Prakadan et al.   NATURE REVIEWS GENETICS

Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture

(2017) Liam Walker et al.   PLANT CELL

Plant Systems Biology at the Single-Cell Level

(2017) Marc Libault et al.   TRENDS IN PLANT SCIENCE

Abiotic Stress Signaling and Responses in Plants

(2016) Jian-Kang Zhu   CELL

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

(2016) P. L. Stahl et al.   SCIENCE

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

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

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Plant transcriptomics and responses to environmental stress: an overview

(2015) SAMEEN RUQIA IMADI et al.   JOURNAL OF GENETICS

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

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

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

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

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

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

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

(2011) Hinako Takehisa et al.   PLANT JOURNAL

High-throughput microfluidic single-cell RT-qPCR

(2011) A. K. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

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