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

Cell Atlas technologies and insights into tissue architecture

(2020) Anna Wilbrey-Clark et al.   BIOCHEMICAL JOURNAL

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

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

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

Visualization of spatial gene expression in plants by modified RNAscope fluorescent in situ hybridization

(2020) Shyam Solanki et al.   Plant Methods

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

(2020) Zhixin Liu et al.   Molecular Plant

Prototypical pacemaker neurons interact with the resident microbiota

(2020) Alexander Klimovich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell transcriptomic analysis identifies the conversion of zebrafish Etv2-deficient vascular progenitors into skeletal muscle

(2020) Brendan Chestnut et al.   Nature Communications

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

(2020) Alma Andersson et al.   Communications Biology

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

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

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

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

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

(2019) Xiaoyan Qian et al.   NATURE METHODS

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

(2019) Michaela Asp et al.   CELL

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays

(2018) Stefania Giacomello et al.   Nature Protocols

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

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

(2017) Naomi Habib et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles

(2017) Jordi Moreno-Romero et al.   Nature Protocols

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Massively parallel digital transcriptional profiling of single cells

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

Laser Capture Microdissection Protocol for Xylem Tissues of Woody Plants

(2017) Olga Blokhina et al.   Frontiers in Plant Science

Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation

(2017) Robert Ietswaart et al.   Cell Systems

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

(2016) Song Li et al.   DEVELOPMENTAL CELL

A method for detecting single mRNA molecules in Arabidopsis thaliana

(2016) Susan Duncan et al.   Plant Methods

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

(2016) P. L. Stahl et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

(2016) Stefanie Rosa et al.   Nature Communications

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

(2015) Evan Z. Macosko et al.   CELL

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

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

The use of fluorescence-activated cell sorting in studying plant development and environmental responses

(2013) Anthony D. Carter et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

(2010) Roger B. Deal et al.   DEVELOPMENTAL CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS