Mapping Single Cells Back to the Tissue

Characterizing the transcriptomic profiles of individual cells by single-cell RNA sequencing (scRNA-Seq) has become a universal tool to identify both known and novel cell types and to understand tissue structure and function, ushering in a new era of single cell biology. This has proven to be especially true in complex organs and tissues with high cellular heterogeneity, such as mammalian brain and tumors. However, scRNA-Seq utilizes dissociated cells and results in the loss of spatial organization of the cell population being analyzed. It is therefore essential to complement scRNA-seq analysis with methods such as RNA in situ hybridization (ISH) in order to obtain visual confirmation of both single cell and spatial gene expression.

RNAscopeTM assays are robust, highly specific and sensitive multiplex RNA ISH assays that allow you to visualize high throughput single cell transcriptomic results. Multiplex up to four assays to co-localize up to four specific markers at the single cell level (can combine with IHC). These assays allow you to visually confirm individual gene and gene signature expression profiles within a single cell, thereby validating transcriptomic findings. They also allow you to spatially localize cell types and states in their intact tissue environment, thus mapping cell type-specific gene expression profiles back to the tissue context of complex and heterogeneous organs and tumors.

The Power of In Situ Transcriptomics

Single Cell Analysis - Detection of glutamatergic and GABAergic neurons in mouse brain

Watch scientists describe the power of in situ transcriptomics and discuss the application of this technology to large-scale tissue mapping in the mouse brain. They explain how RNAscope Multiplex Fluorescence assays complement single cell RNA sequencing. 

Science Webinar Series: Harnessing in situ transcriptomics to reveal complex tissue architecture at single-cell resolution.
Omer Bayraktar, Ph.D., Wellcome Sanger Institute, Hinxton, U.K.

Knowledge Resource Series: Spatial Mapping and Confirmation of Diverse Gene Signatures Using the Multiplexed Single-Cell Approach of RNAscope Assay.

Jyoti Phatak-Sheldon, MS
Associate Scientist - Applications, Advanced Cell Diagnostics


Complement Single Cell RNA Sequencing with RNAscope Assays

A rapidly increasing number of researchers are publishing in prominent journals using RNAscope assays to spatially map scRNA-Seq results.



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Reveal Single-Cell Insights in Spatial Context with RNAscope™ ISH Assays.

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Single cell Spatial RNAscope Publications

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Recent Single Cell Articles


Application Note

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Easy to Start with the RNAscope Assay Intro Packs

New to RNAscope assays? You can visualize any RNA target from any species in any tissue in just one day. Start by selecting a RNAscope Assay Intro Pack that has everything you need to run your first assay. Then select the RNAscope Probe that is specific to your RNA target of interest. These intro packs can also be used for multiplex assays, detecting more than one RNA target at a time. Contact one of our RNAscope assay scientist to help address your research needs.

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Promotions for New Users

New User Program – FREE!

For first-time users, we offer the opportunity for a RNAscope Assay scientist to personally assist you with setting up your first assay. Our team of scientists are ready to support you in getting superior results from our RNAscope™ assays.

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