Reveal Transcriptomic Insights in Spatial Context with RNAscope

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Transcriptomic technologies such as single cell RNA sequencing (scRNA-Seq), single-nuclei, or bulk-sequencing have revolutionized the study of cellular diversity, enabling researchers to identify known and novel cell types and gain insights into tissue structure and function.

However, such transcriptomic methodologies require cell dissociation, which disrupts the spatial context of the cells. To address this limitation, it is crucial to pair molecular information with spatially-resolved methods like RNA in situ hybridization (ISH). Using RNAscope™ ISH allows for the visualization of gene expression within the intact tissue, preserving the spatial organization and providing a more comprehensive understanding of cellular functions, individual cell profiles, and their spatial arrangements, enhancing our ability to study and interpret complex biological systems.

Single Cell Spatial Workflow

Illustration of spatial characterization of single cell seq-identified phenotypes in mouse brain

Figure 1. Spatial characterization of single cell seq-identified phenotypes. Data from mouse brain single cell sequencing followed by RNAscope validation.

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Applications

Spatial Mapping

Validate the presence, abundance, and spatial localization of novel cell subtypes and cell markers.

View Nature Article

Cellular Dynamics

Identify meaningful changes in cell phenotypes and cell-cell interactions in human pathology and animal models.

View Nature Article

Activation States

Visualize changes in single-cell function including initiation of signaling pathways and transcriptional activation.

View Cell Article

Validate Gene Signatures with Spatial Context at the Single Cell Level

Visualizing striatal Drd1a and Drd2 medium spiny neurons (MSNs) using the RNAscope HiPlex assay for 12 targets in fresh frozen mouse brain sections.

Targets are Drd1a, Drd2, Foxp1, Pcdh8, Synpr, Htr7, Meis, Calb1, Crym, Cnr1, Wfs1, and TH.

Drd1a

Synpr

Crym

Drd2

Htr7

Cnr1

Foxp1

Meis

Wfs1

Pcdh8

Calb1

Clear selection

Getting Started is Easy

1. Easy Probe Selection

Select just the genes you want from an extensive online catalog and custom design services.

2. No Spatial Instrument Required

Get results quickly using RNAscope manual kits and your own fluorescent microscope. Easily scale with automated protocols.

3. Expert Technical Support

Our experienced technical specialists in RNA spatial imaging will help you get up and running quickly.

Customer Success Stories

Ruchi Komal PhD, Research Fellow
SLCR, National Institute of Mental Health, NIH

RNAscope spatial analysis greatly improves our research by offering high-resolution visualization of gene expression within the SCN... validating discoveries from single-cell data, identifying rare cell populations, and facilitating gene co-expression analysis in situ.

Samuel Marsh, PhD and Connor Dufort
Lab of Dr. Beth Stevens, Boston Children’s Hospital

We love the RNAscope HiPlex assay! RNAscope was already an integral part to our workflows to evaluate and validate the results we get from single cell sequencing experiments. The capabilities of the HiPlex assay allow us to visualize several different cell types and/or states in the same slice of tissue which provides critical information on spatial distribution and relationships. The protocol worked exactly as advertised and very similar to current multiplex RNAscope. Additionally, the free ACD image registration software worked like a charm and was very straightforward to align all of the images from multiple rounds of imaging.

Prithviraj Rajebhosale, PhD
Research Fellow, NINDS, NIH

My single-cell transcriptomic experiments have focused on uncovering and understanding the molecular makeup of cellular heterogeneity in the rodent brain. The RNAscope HiPlex assay provided the much-needed flexibility for this project. It allowed me to quickly validate tens of targets and their co-expression.

Featured Resources

Speaker: Jonathan Chen, MD, PhD Director, Massachusetts General Hospital

Webinar: Spatial Organization of Multicellular Immune Hubs in Human Colorectal Cancer

In this webinar, Dr Jon Chen, Massachusetts General Hospital Cancer Center, Harvard Medical School, will discuss this study in greater detail and demonstrate a path to discovering multicellular interaction networks that underlie immunologic and tumorigenic processes in human cancer.

Learning Objectives:

How scRNA-seq can be used to reveal shared and distinct features of human MMRd and MMRp colorectal cancer
How multicellular immune hubs can be predicted based on co-variation of gene programs
Why understanding the molecular mechanisms underlying immune hubs and their temporal and spatial regulation upon treatment is critical for advancing cancer therapy

Watch Webinar

Incorporating RNAscope HiPlex Assay into single cell RNA sequencing workflows

Reveal Transcriptomic Insights in Spatial Context

Single Cell Spatial Workflow