A technical review and guide to RNA fluorescence in situ hybridization

Hox gene expression in postmetamorphic juveniles of the brachiopod Terebratalia transversa

(2019) Ludwik Gąsiorowski et al.   EvoDevo

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

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

Visualizing neuroinflammation with fluorescence and luminescent lanthanide-based in situ hybridization

(2019) Lindsay M. Parker et al.   Journal of Neuroinflammation

High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules

(2019) Salvatore A. E. Marras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species

(2018) Chiara Sinigaglia et al.   DEVELOPMENTAL BIOLOGY

Detection of Coxiella burnetii in heart valve sections by fluorescence in situ hybridization

(2018) Karin Aistleitner et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria

(2018) Rui Rocha et al.   PLoS One

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific Fluorescence in Situ Hybridization (FISH) Test to Highlight Colonization of Xylem Vessels by Xylella fastidiosa in Naturally Infected Olive Trees (Olea europaea L.)

(2018) Massimiliano Cardinale et al.   Frontiers in Plant Science

A PCR-Based Method for RNA Probes and Applications in Neuroscience

(2018) Ruifang Hua et al.   Frontiers in Neuroscience

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges

(2018) Xavier Pichon et al.   MOLECULAR CELL

ImmunoFISH: Simultaneous Visualisation of Proteins and DNA Sequences Gives Insight Into Meiotic Processes in Nuclei of Grasses

(2018) Adél Sepsi et al.   Frontiers in Plant Science

Mapping Neurotransmitter Identity in the Whole-Mount Drosophila Brain Using Multiplex High-Throughput Fluorescence in Situ Hybridization

(2018) Geoffrey W. Meissner et al.   GENETICS

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Molecular characterization of vasa homologue in marbled goby, Oxyeleotris marmorata: Transcription and localization analysis during gametogenesis and embryogenesis

(2018) Wei Liu et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Simultaneous detection of the subcellular localization of RNAs and proteins in cultured cells by combined multicolor RNA-FISH and IF

(2017) Cindy Meyer et al.   METHODS

FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry

(2017) Riccardo Arrigucci et al.   Nature Protocols

Imaging mRNA and protein interactions within neurons

(2017) Carolina Eliscovich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties

(2017) Sabrina M. Schiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new method for real-time evaluation of pepsin digestion of paraffin-embedded tissue sections, prior to fluorescence in situ hybridisation

(2017) Xiaojing Teng et al.   VIRCHOWS ARCHIV

itFISH: Enhanced Staining by Iterative Fluorescent In Situ Hybridization

(2017) Richard H. Row et al.   Zebrafish

Pre-culture Sudan Black B treatment suppresses autofluorescence signals emitted from polymer tissue scaffolds

(2017) Lin Qi et al.   Scientific Reports

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

(2017) Allison Jandura et al.   Jove-Journal of Visualized Experiments

Visualizing Multiciliated Cells in the Zebrafish Through a Combined Protocol of Whole Mount Fluorescent In Situ Hybridization and Immunofluorescence

(2017) Amanda N. Marra et al.   Jove-Journal of Visualized Experiments

Mapping a multiplexed zoo of mRNA expression

(2016) Harry M. T. Choi et al.   DEVELOPMENT

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

(2016) Prasath Thiruketheeswaran et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Fluorescent whole-mount RNA in situ hybridization (F-WISH) in plant germ cells and the fertilized ovule

(2016) Andrea Bleckmann et al.   METHODS

mRNA quantification using single-molecule FISH in Drosophila embryos

(2016) Tatjana Trcek et al.   Nature Protocols

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Double In situ Hybridization for MicroRNAs and mRNAs in Brain Tissues

(2016) Atsushi Kasai et al.   Frontiers in Molecular Neuroscience

Multi-target Chromogenic Whole-mount In Situ Hybridization for Comparing Gene Expression Domains in Drosophila Embryos

(2016) Giselbert Hauptmann et al.   Jove-Journal of Visualized Experiments

A Whole Mount In Situ Hybridization Method for the Gastropod Mollusc Lymnaea stagnalis

(2016) Daniel J. Jackson et al.   Jove-Journal of Visualized Experiments

The developmental basis for the recurrent evolution of deuterostomy and protostomy

(2016) José M. Martín-Durán et al.   Nature Ecology & Evolution

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Prediction of melting temperatures in fluorescencein situhybridization (FISH) procedures using thermodynamic models

(2015) Sílvia Fontenete et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging

(2015) Etsuo A Susaki et al.   Nature Protocols

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Whole-mount single molecule FISH method for zebrafish embryo

(2015) Yuma Oka et al.   Scientific Reports

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

(2014) Harry M. T. Choi et al.   ACS Nano

Detection ofALKrearrangements in malignant pleural effusion cell blocks from patients with advanced non-small cell lung cancer: A comparison of Ventana immunohistochemistry and fluorescence in situ hybridization

(2014) Weiya Wang et al.   CANCER CYTOPATHOLOGY

Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization

(2014) Kazuki Tainaka et al.   CELL

Whole-mount fluorescentin situhybridization staining of the colonial tunicateBotryllus schlosseri

(2014) Adam D. Langenbacher et al.   GENESIS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Whole-Mount MeFISH: A Novel Technique for Simultaneous Visualization of Specific DNA Methylation and Protein/RNA Expression

(2014) Hirosuke Shiura et al.   PLoS One

Unexpected DNA Loss Mediated by the DNA Binding Activity of Ribonuclease A

(2014) Federico Donà et al.   PLoS One

Single  -Actin mRNA Detection in Neurons Reveals a Mechanism for Regulating Its Translatability

(2014) A. R. Buxbaum et al.   SCIENCE

ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue

(2013) T. Kuwajima et al.   DEVELOPMENT

mRNA fluorescence in situ hybridization to determine overlapping gene expression in whole-mount mouse embryos

(2013) Stanley J. Neufeld et al.   DEVELOPMENTAL DYNAMICS

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

(2013) Samuel O Skinner et al.   Nature Protocols

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

(2013) Sydney M. Shaffer et al.   PLoS One

Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo

(2013) Alistair Nicol Boettiger et al.   Cell Reports

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

(2013) Félix Legendre et al.   Jove-Journal of Visualized Experiments

The vanadyl ribonucleoside complex inhibits ribosomal subunit formation in Staphylococcus aureus

(2012) A. D. Frazier et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Optimization of DNA Hybridization Efficiency by pH-Driven Nanomechanical Bending

(2012) Jiayun Zhang et al.   LANGMUIR

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

(2012) Magda Bienko et al.   NATURE METHODS

RNA imaging in situ

(2012) Monya Baker   NATURE METHODS

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Single-mRNA counting using fluorescent in situ hybridization in budding yeast

(2012) Tatjana Trcek et al.   Nature Protocols

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

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

Two-color fluorescent in situ hybridization in the embryonic zebrafish brain using differential detection systems

(2011) Gilbert Lauter et al.   BMC DEVELOPMENTAL BIOLOGY

The maintenance and regeneration of the planarian excretory system are regulated by EGFR signaling

(2011) J. C. Rink et al.   DEVELOPMENT

The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii

(2011) Patrick R. H. Steinmetz et al.   EVOLUTION & DEVELOPMENT

Peripheral sensory cells in the cephalic sensory organs of Lymnaea stagnalis

(2011) Russell C. Wyeth et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Antigen Retrieval Causes Protein Unfolding

(2011) Carol B. Fowler et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Multicolor fluorescent in situ hybridization to define abutting and overlapping gene expression in the embryonic zebrafish brain

(2011) Gilbert Lauter et al.   Neural Development

Formalin Fixation at Low Temperature Better Preserves Nucleic Acid Integrity

(2011) Gianni Bussolati et al.   PLoS One

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics

Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting

(2009) Adam Paré et al.   CURRENT BIOLOGY

Formaldehyde-based whole-mount in situ hybridization method for planarians

(2009) Bret J. Pearson et al.   DEVELOPMENTAL DYNAMICS

FISH glossary: an overview of the fluorescence in situ hybridization technique

(2008) Emanuela V. Volpi et al.   BIOTECHNIQUES

Acoel development indicates the independent evolution of the bilaterian mouth and anus

(2008) Andreas Hejnol et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

An optimized procedure for whole-mount in situ hybridization on mouse embryos and embryoid bodies

(2008) Denis Piette et al.   Nature Protocols