Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants

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

(2021) Xiaosa Xu et al.   DEVELOPMENTAL CELL

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

Serial Block-Face Scanning Electron Microscopy Reveals That Intercellular Nuclear Migration Occurs in Most Normal Tobacco Male Meiocytes

(2021) Sergey Mursalimov et al.   Frontiers in Plant Science

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

Bridging Genomics and Tissue Pathology

(2020) Nikhil Rao et al.   Genetic Engineering & Biotechnology News

Imaging flowers: a guide to current microscopy and tomography techniques to study flower development

(2020) Nathanaël Prunet et al.   JOURNAL OF EXPERIMENTAL BOTANY

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

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

Does Gene Expression Noise Play a Functional Role in Plants?

(2020) Sandra Cortijo et al.   TRENDS IN PLANT SCIENCE

Genetically encoded X-ray cellular imaging for nanoscale protein localization

(2020) Huating Kong et al.   National Science Review

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Visual and hydraulic techniques produce similar estimates of cavitation resistance in woody species

(2020) Alice Gauthey et al.   NEW PHYTOLOGIST

Non-invasive imaging reveals convergence in root and stem vulnerability to cavitation across five tree species

(2020) Jennifer M R Peters et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

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

Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution

(2019) Jana Bürgers   Neurophotonics

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

Defining the developmental program leading to meiosis in maize

(2019) Brad Nelms et al.   SCIENCE

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

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

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

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

Transcriptional Activation of Arabidopsis Zygotes Is Required for Initial Cell Divisions

(2019) Ping Kao et al.   Scientific Reports

Towards an integrative understanding of stamen–corolla tube modifications and floral architecture in Boraginaceae s.s. (Boraginales)

(2019) Julius Jeiter et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

(2018) Kim Wong et al.   BIOINFORMATICS

Gynoecium and Fruit Development in Heliotropium Sect. Heliothamnus (Heliotropiaceae)

(2018) Julius Jeiter et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Ultrastructural localisation of protein interactions using conditionally stable nanobodies

(2018) Nicholas Ariotti et al.   PLOS BIOLOGY

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

(2018) Stefania Giacomello et al.   Nature Protocols

Differential growth and shape formation in plant organs

(2018) Changjin Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Advances in Imaging Plant Cell Dynamics

(2017) George Komis et al.   PLANT PHYSIOLOGY

Light sheet microscopy and live imaging of plants

(2016) BÉATRICE BERTHET et al.   JOURNAL OF MICROSCOPY

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

(2016) P. L. Stahl et al.   SCIENCE

Analysis of cell division patterns in theArabidopsisshoot apical meristem

(2015) Bruce E. Shapiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Metabolism and development - integration of micro computed tomography data and metabolite profiling reveals metabolic reprogramming from floral initiation to silique development

(2013) Anke Bellaire et al.   NEW PHYTOLOGIST

Histological and Micro-CT Evidence of Stigmatic Rostellum Receptivity Promoting Auto-Pollination in the Madagascan Orchid Bulbophyllum bicoloratum

(2013) Alexander Gamisch et al.   PLoS One

Plant Tissues in 3D via X-Ray Tomography: Simple Contrasting Methods Allow High Resolution Imaging

(2013) Yannick M. Staedler et al.   PLoS One

Three-dimensional geometric morphometrics for studying floral shape variation

(2010) Timotheüs van der Niet et al.   TRENDS IN PLANT SCIENCE

Plant structure visualization by high-resolution X-ray computed tomography

(2010) Stijn Dhondt et al.   TRENDS IN PLANT SCIENCE

A new preparation method to study fresh plant structures with X-ray computed tomography

(2009) O. LEROUX et al.   JOURNAL OF MICROSCOPY

Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X-ray computed tomography

(2008) Eli Kaminuma et al.   PLANT JOURNAL