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Choosing single-cell and spatial analysis technologies

The number of different technologies and hardware platforms that are now on the market can be overwhelming. Each comes with its own advantages and caveats, and often some are suited to solve a specific problem more than others. Considering which platform is the best for your particular research is critically important to get the most of your precious samples and generate the best data for your research questions.

10x Genomics

10x Genomics are industry leaders in the single-cell and spatial analysis space. With their products published in over 3500 original research articles, 10x Genomics offer comprehensive workflows with everything from reagents to instruments and analysis software.

Xenium In Situ

The Xenium In Situ platform from 10x Genomics enables high throughput subcellular mapping of 100s of RNA targets, revealing new insights into cellular structure and function. The platform includes a versatile and easy-to-use instrument, sensitive and specific chemistry, and a diverse menu of customisable panels.

Xenium In Situ (Image: 10x Genomics)

Chromium X

Chromium X is the flagship instrument for all things single-cell from 10x Genomics. The Chromium X is compatible will all 10x Genomics chemistry and reagent kits allowing single-cell gene expression, immune profiling, ATAC chromatin accessibility and targeted gene expression.

Chromium X (Image: 10x Genomics)

Visium spatial gene expression and spatial proteogenomics

10x Genomics offer Visium spatial gene expression for next-generation molecular profiling and tissue classifying based on total mRNA. This technology allows the whole transcriptome to be mapped from FFPE or fresh frozen tissue sections, while at the same time retaining the morphological context.

Visium spatial proteogenomics provides tissue profiling with transcriptomics and protein co-detection. This technology combines whole transcriptome spatial analysis with immunofluorescence protein detection in the same tissue section. Spatial proteogenomics gives a deeper understanding of tissue organisation with co-localised protein detection and gene expression analysis.

Visium CytAssist

Compatible with both Visium spatial gene expression and spatial proteogenomics, Visium CytAssist is designed to simplify workflows by transfering analytes from standard glass slides to Visium slides, enabling spatial profiling from an expanded range of sample types.

Visium CytAssist (Image: 10x Genomics)

An overview of single-cell RNA sequencing and spatial transcriptomics

NanoString

NanoString are pioneers within the field of spatial biology, providing solutions, workflows and products for spatial transcriptomics, spatial proteomics and single-cell spatial multi-omics.

GeoMx® Digital Spatial Profiler

The GeoMx Digital Spatial Profiler workflow integrates with current histological or genomics workflows to generate spatial multi-omics data. Whole tissue sections (FFPE or fresh frozen) can be imaged and stained with assays for RNA and protein. Specific tissue compartments or cell types can be selected, and expression levels subsequently quantified using a NanoString nCounter Analysis System or an Illumina Sequencer.

Nanostring GeoMx Digital Spatial Profiler workflow (Image: NanoString)

CosMx™ Spatial Molecular Imager

The CosMx Spatial Molecular Imager from NanoString is a high-plex in situ analysis platform that can perform spatial multi-omics using FFPE or fresh frozen tissue samples at a single cell and sub-cellular resolution. This platform enables rapid quantification and visualisation of up to 1,000 RNA and 100 validated protein analytes.

Potential applications include cell atlases, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery.

Nanostring CosMx Spatial Molecular Imager workflow (Image: NanoString)

Mission Bio

Mission Bio are a single-cell commercial provider that offer multi-omic solutions for application within oncology and precision medicine. The Tapestri Platform from Mission Bio is designed for single-cell multi-omics, providing both genotype and phenotype data from the same cell.

Tapestri Platform

The Tapestri Platform from Mission Bio is designed for single-cell multi-omics, providing both genotype and phenotype data from the same cell. Using a novel two-step microfluidic workflow, the Tapestri Platform can access DNA and protein in single cells to give a true multiomics picture. A complete solution is offered with core kits to go from single cells to a sequencing ready library and analysis tools. Targeted, customisable content for oncology and gene therapy applications are also available.

Tapestri Platform (Image: Mission Bio)

Other suppliers of kits and reagents

Report: The 2023 Spatial and Single-cell Analysis Playbook

A guide to single-cell sequencing and spatial analysis