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Fluorescence in situ hybridization (FISH) is a method to localize nucleic acid targets in fixed cells for cytogenetic or gene expression studies. It relies on fluorophore-labelled DNA or RNA probes to count and localize specific genes or regions along chromosomes, detect mutations, or analyze temporal and spatial gene expression.
Application of multiplexed RNA in situ mapping techniques to human tissues remains challenging. Here, the authors report DART-FISH, a padlock probe-based technology capable of profiling large numbers of genes in centimetre-sized human tissue sections.
Leveraging the fact that eukaryotic genomes are organized into gene modules, FISHnCHIPs images multiple co-expressed genes simultaneously for sensitive and high throughput profiling of gene programs and cell types in tissues.
This study introduces a new multiplexed fluorescence in situ hybridization method, PHYTOMap, that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost.
Gene selection for spatial transcriptomics is currently not optimal. Here the authors report PERSIST, a flexible deep learning framework that uses existing scRNA-seq data to identify gene targets for spatial transcriptomics; they show this allows you to capture more information with fewer genes.
Methods for analysing spatial gene expression in plants have been limited in their throughput. Now the imaging method PHYTOMap allows the spatial expression of dozens of genes to be analysed in three-dimensional whole-mount tissue at single-cell resolution, in a transgene-free manner.
An approach combining in situ tagmentation and transcription with MERFISH enables spatial profiling of the epigenome in tissues with single-cell resolution.
Researchers use electric fields to transfer RNA from a tissue sample onto a surface for subsequent fluorescence in situ hybridization-based profiling of transcriptomes at the single-cell level.
Composite in situ imaging leverages gene expression patterns to improve the efficiency of highly multiplexed single-molecule FISH measurements by orders of magnitude.
A study in Cell presents a new approach that increases resolution and throughput compared with existing imaging methods and provides insights into the relationship between transcription and the 3D genome.
