Research Solutions: Spatial Validation of Single-Cell Transcriptomes

Single Cell Analysis - Spatial Validation of Single Cell Transcriptome

Single Cell Analysis - Spatial Validation of Single Cell Transcriptome

Detection of glutamatergic and GABAergic neurons in mouse brain

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

Detection of glutamatergic and GABAergic neurons in mouse brain (40x Zoom)

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

Single Cell Analysis - Detection of different cell populations simultaneously in mouse brain

Single Cell Analysis - Detection of different cell populations simultaneously in mouse brain

Simultaneous detection of 3 intestinal cell populations

Single Cell Analysis - Simultaneous detection of 3 intestinal cell populations

Identification of distinct intestinal cell populations

Identification of distinct intestinal cell populations

Initiatives such as the Human Cell Atlas (HCA) require assessing gene expression at the single cell level, however current single-cell transcriptome studies utilize dissociated cells and result in the loss of spatial organization of the cell population in the tissue contest. Validation and spatial mapping of single-cell analyses can be obtained using assays that retain spatial organization, such as RNA in situ hybridization (ISH). The RNAscope® technology is a robust, highly specific and sensitive RNA ISH methodology with multiplexing capabilities to validate and provide spatial information for high-throughput single cell transcriptomic results. This technology allows for cell type-specific expression profiles to be mapped back to the complex tissue context of organs. Benefits of the RNAscope® technology include:

  • Visual confirmation of individual gene and gene signature expression
  • Single cell resolution of gene expression and co-localization
  • Spatial localization of cell types and states in tissue environment
  • Identifying proper single cells for quality transcriptome analysis

Publications

With over 1500 total RNAscope® publications (including 35 to date using the assay to validate single-cell RNAseq results), the RNAscope® technology is a highly regarded methodology for mapping expression profiles to the tissue context.

A Single-Cell Survey of the Small Intestinal Epithelium - Aviv Regev, an HCA member from the Broad Institute at MIT, and colleagues recently published their work profiling the mouse small intestinal epithelium at the single cell level. RNAseq transcriptome profiling of 53,193 individual epithelial cells enabled the identification and characterization of previously unknown subtypes of intestinal epithelial cell and their gene signatures, and the RNAscope® Multiplex assay was used to validate all of their major findings.

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq - Steve Quake, another HCA member from Stanford University, and colleagues performed unbiased and comprehensive single-cell profiling of the developing mouse lung and then used the RNAscope® Multiplex assay to validate and map previously unknown markers in individual cells in the tissue context.

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity - Maria Kasper and colleagues at the Karolinska Institute identified 25 individual cell populations in the mouse hair follicle, and combined the RNAscope® ISH with IHC to confirm the spatial mapping of these cell populations within the hair follicle.

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell type - Patrick Ernfors and colleagues at the Karolinska Institute identified 15 glutamatergic excitatory and 15 GABAergic inhibitory neurons organized in a multilayered pattern defined by cell type in the mouse spinal cord. Spatial transcriptomics with the RNAscope® Multiplex ISH revealed an organizational pattern of neuronal subtypes in multiple discrete layers.

Seeing is Believing!

Let us show you how the RNAscope® Assay can validate your scRNA-seq data and provide powerful spatial information within tissue.

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