4.6 Article

A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

A pan-grass transcriptome reveals patterns of cellular divergence in crops

Bruno Guillotin et al.

Summary: Comparative analysis of root cell transcriptomes in three grass species reveals that some cell types diverged more rapidly, driven by recruitment of gene modules from other cell types. The recent whole-genome duplication provides new, highly localized gene expression domains that favour fast-evolving cell types. Cell-by-cell comparative analysis can extract conserved modules and provide insight on the evolution of cells mediating key functions in crops.

NATURE (2023)

Article Plant Sciences

An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells

Reinout Laureyns et al.

Summary: The study optimized in situ sequencing (ISS) to simultaneously locate the transcripts of 90 genes in maize shoot apex, providing highly comparable expression profiles and allowing discrimination between tissue domains. The use of ISS in the shoot apex revealed spatiotemporal transcriptional events. The expression patterns of PLASTOCHRON1 (PLA1) demonstrated the effectiveness of the technology in identifying specific gene expression at cell boundaries. Spatial transcriptomics has significant applications in plant developmental biology research.

PLANT PHYSIOLOGY (2022)

Article Cell Biology

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

Keke Xia et al.

Summary: This study presents a single-cell spatial transcriptome profiling technique called scStereo-seq, which successfully characterized the transcriptomic differences between upper and lower epidermal cells in Arabidopsis leaves. The study also discovered cell-type-specific gene expression gradients and spatial developmental trajectories of vascular cells and guard cells.

DEVELOPMENTAL CELL (2022)

Article Developmental Biology

Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization

Maayan Schwarzkopf et al.

Summary: This technology utilizes the HCR mechanism to achieve multiplexed, quantitative, high-resolution RNA imaging in highly autofluorescent samples, while also enabling accurate and precise protein relative quantitation in immunohistochemistry.

DEVELOPMENT (2021)

Review Biochemistry & Molecular Biology

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

Rahul Shaw et al.

Summary: The adoption of single-cell RNA sequencing technology has revolutionized the transcriptome analysis, allowing for better understanding of tissue and cellular heterogeneity and rapid identification of rare cell types. In the field of plant sciences, single-cell transcriptome profiling is in its early stages and presents exciting challenges to overcome.

MOLECULAR PLANT (2021)

Article Plant Sciences

A ClearSee-Based Clearing Protocol for 3D Visualization of Arabidopsis thaliana Embryos

Ayame Imoto et al.

Summary: The ClearSee tissue clearing method is reliable for studying embryo morphology and gene expression patterns in Arabidopsis thaliana, enabling high-quality 3D imaging with cellular resolution.

PLANTS-BASEL (2021)

Article Multidisciplinary Sciences

Ground tissue circuitry regulates organ complexity in maize and Setaria

Carlos Ortiz-Ramirez et al.

Summary: A cell-resolution map of maize root was generated using single-cell RNA sequencing, revealing an alternative configuration of the tissue formative transcription factor SHR. The study shows that the SHR pathway controls the expansion of cortical tissue, impacting the anatomical complexity of plants.

SCIENCE (2021)

Review Plant Sciences

Advances and Opportunities in Single-Cell Transcriptomics for Plant Research

Carolin Seyfferth et al.

Summary: The advancements in single-cell technologies are rapidly expanding applications in plant biology, providing comprehensive guidelines from sample preparation to data analysis. These technologies will accelerate and shape plant-specific research in the near future.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021 (2021)

Review Plant Sciences

Advances in Two-Photon Imaging in Plants

Yoko Mizuta

Summary: Two-photon excitation microscopy (2PEM) allows deep imaging of living tissues with reduced autofluorescence compared to confocal microscopy, achieving higher resolution. Fluorescent proteins with long emission wavelengths, such as orange-red fluorescent proteins, are suitable for high-quality two-photon live imaging in plants.

PLANT AND CELL PHYSIOLOGY (2021)

Review Multidisciplinary Sciences

A technical review and guide to RNA fluorescence in situ hybridization

Alexander P. Young et al.

Review Biochemical Research Methods

Tutorial: guidance for quantitative confocal microscopy

James Jonkman et al.

NATURE PROTOCOLS (2020)

Article Multidisciplinary Sciences

TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T

Yang Zhu et al.

NATURE COMMUNICATIONS (2020)

Article Developmental Biology

Mapping a multiplexed zoo of mRNA expression

Harry M. T. Choi et al.

DEVELOPMENT (2016)

Article Biochemical Research Methods

A method for detecting single mRNA molecules in Arabidopsis thaliana

Susan Duncan et al.

PLANT METHODS (2016)

Article Multidisciplinary Sciences

An epidermis-driven mechanism positions and scales stem cell niches in plants

Jeremy Gruel et al.

SCIENCE ADVANCES (2016)

Article Biochemical Research Methods

Protocol: an improved and universal procedure for whole-mount immunolocalization in plants

Taras Pasternak et al.

PLANT METHODS (2015)

Article Chemistry, Multidisciplinary

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

Harry M. T. Choi et al.

ACS NANO (2014)

Article Biochemical Research Methods

Analysis of 3D gene expression patterns in plants using whole-mount RNA in situ hybridization

Frederique Rozier et al.

NATURE PROTOCOLS (2014)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Biotechnology & Applied Microbiology

Programmable in situ amplification for multiplexed imaging of mRNA expression

Harry M. T. Choi et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

TERMINAL FLOWER1 is a mobile signal controlling Arabidopsis architecture

Lucio Conti et al.

PLANT CELL (2007)

Article Biochemical Research Methods

In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples

Jan Hejatko et al.

NATURE PROTOCOLS (2006)

Article Biochemical Research Methods

In situ hybridization for mRNA detection in Arabidopsis tissue sections

Philip B. Brewer et al.

NATURE PROTOCOLS (2006)

Review Genetics & Heredity

Molecular mechanisms of flower development: An armchair guide

BA Krizek et al.

NATURE REVIEWS GENETICS (2005)

Article Multidisciplinary Sciences

Triggered amplification by hybridization chain reaction

RM Dirks et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Biochemistry & Molecular Biology

Giving meaning to movement

MK Barton

Article Developmental Biology

Initiation of axillary and floral meristems in Arabidopsis

J Long et al.

DEVELOPMENTAL BIOLOGY (2000)