RNAscope™ Multiplex Fluorescent Assays

Multiomics has begun to take the center stage in biomedical research as it combines two or more individual omics studies such as genomics, epigenomics, transcriptomics, proteomics, and metagenomics, allowing scientists to interpret and visualize the mechanisms of biological processes with spatial context.

In this free guide, we present a series of case studies illustrating how a multi-omic multiplexing approach can be leveraged to gain a comprehensive view of spatial biology, including a multiplexed in situ transcriptomic method for the spatial mapping of target genes in highly complex and heterogenous FFPE tumor tissues, and much more.

This application note demonstrates the concordance between the RNAscopeTM and GeoMx® assays and highlights the detailed molecular analysis that can be performed with this type of high-plex spatial data. Also described are qualified RNAscopeTM probe combinations selected for cell type markers shown to be compatible with the GeoMx® CTA assay.

In this application note, Advanced Cell Diagnostics (ACD) provides examples of exemplary assays, discusses experimental considerations, addresses common challenges, introduces HALO® image analysis solutions, and answers common quantitative image analysis questions. Plus, learn how RNAscopeTM technology is designed to enable RNA target expression analysis within intact cells and tissues with high sensitivity and specificity.

In this application note, the diverse cell types in the mouse striatum that have been previously identified by scRNA-seq were confirmed and spatially mapped using the RNAscopeTM Multiplex Fluorescent assay and the RNAscopeTM HiPlex assay. The major and minor gene signatures identified by scRNA-seq, including discrete D1 and D2 medium spiny neuron (MSN) subtypes, were confirmed.

Further cellular heterogeneity within the MSN subpopulations was marked by a transcriptional gradient, which was spatially resolved with the RNAscopeTM technology.

The RNAscope® Duplex and Multiplex assays enable simultaneous detection of more than one target RNA thus facilitating the evaluation of multiple cell phenotypes and spatial relationships within a complex tissue microenvironment. Download the guide below to find out how HALO® imaging software can create an easier solution with RNAscope® assays.

RNA plays an important role in the regulation of cellular processes, making it an ideal biomarker for dynamic gene expression changes in both healthy cells and disease phenotypes. In situ hybridization (ISH) technology provides a powerful method to detect this gene expression, at single-cell resolution, within the spatial and morphological context of an intact tissue. Advanced Cell Diagnostics offer a comprehensive portfolio of ISH assays, with various levels of plexing, that can be applied to a wide range of applications, from neuroscience to immuno-oncology to cell therapy.

In this application eBook, we present:

• A series of case studies illustrating the research capabilities of high-plexing assays
• An outline of the benefits of the RNAscope™ technology
• Top tips on how to achieve accurate, reliable results for virtually any target species, tissue, or gene

This application note highlights how the BaseScope ISH assay allows for the visualization of splice junctions between adjacent exons and/or retained introns in order to characterize alternative splicing events in cells and tissues.

In this application note, Advanced Cell Diagnostics discusses the use of the RNAscope® Multiplex Fluorescent assay to visualize the interactions and spatial relationships between immune and tumor cells in tumor microenvironments.

In this application note, Advanced Cell Diagnostics demonstrates the specificity and sensitivity of the RNAscope® in situ hybridization assay as a method to chromogenically and fluorescently examine gene expression with the morphological tissue environment.

In this application note, Advanced Cell Diagnostics demonstrates the utility of the RNAscope® technology in elucidating direct effects of inflammatory cues on intestinal stem cells (ISCs), and their niche, during pathogenesis of intestinal bowel disease (IBD) and other inflammatory diseases.

Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, researchers at the Broad Institute of MIT and Harvard transcriptionally profiled 371,223 cells from human colorectal tumors. Analysis revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, expression programs were identified in different cell types that co-varied across tumors from affected individuals and spatial profiling was used to localize coordinated programs. By identifying interacting cellular programs, the logic underlying spatially organized immune-malignant cell networks was revealed.

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..

Key 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

Certificate of attendance
All webinar participants can request a certificate of attendance, including a learning outcomes summary, for continuing education purposes.

The RNAscope in situ hybridization (ISH) technology is a powerful method for detecting gene expression with spatial and morphological tissue context. In this webinar, we will focus on our Integrated Co-Detection Workflow (ICW), which combines RNAscope ISH technology with immunohistochemistry (IHC) or immunofluorescence (IF) procedures to detect RNA and protein in the same sample. The webinar will cover guidelines for sample preparation, pretreatment, and detection, including tips for troubleshooting.

Key learning objectives

• Overview of RNAscope technologies
• Introduction to the Integrated Co-Detection Workflow (ICW)
• Guidelines on sample preparation and pretreatment
• Guidance on assay setup and appropriate controls
• Troubleshooting tips
• Examples of RNAscope co-detection results

Certificate of attendance
All webinar participants can request a certificate of attendance, including a learning outcomes summary, for continuing education purposes.

Discover how the Wellcome Sanger Institute is helping to develop a physical atlas of all human organs

Learn how a group of MIT researchers are using novel assay technology to better understand anterior thalamic dysfunction

Pushing the spatial genomics frontier one biomolecule at a time from RNA to DNA

Check out the new eBook guide that covers a wide range of higher-plexing applications, from neuroscience to immuno-oncology to cell therapy

In this SelectScience interview, Dr. Arlene Hirano discusses the advantages of using RNAscope HiPlex assays to explore the mammalian retina