Spatial Transcriptomics

What is Spatial Transcriptomics?

Spatial transcriptomics provides a comprehensive roadmap of transcriptional activity within intact tissue sections. Depending on the approach, this method can detect transcriptional activity using hybridization techniques or RNA sequencing (RNA-Seq) technology powered by next-generation sequencing (NGS) with high sensitivity. Regardless of the method, spatial transcriptomics allows you to accurately resolve mRNA expression at the cellular level in structurally preserved tissues.

Spatial Transcriptomics of Complex Tissues

Learn about high-resolution, high-throughput spatial transcriptomics of kidney tissues using the NanoString GeoMx Digital Spatial Profiler and Illumina sequencing systems.

Benefits of Spatial Transcriptomics

A key benefit of spatial transcriptomics is that it provides a topographical arrangement of gene expression patterns mapped onto tissue sections to link structure and activity. This capability allows researchers to articulate biological interactions at the cellular level to gain novel insights into complex tissues, such as tumor microenvironments.

With this method, you’ll be able to chart cellular activity in normal vs. diseased tissues, discover previously unknown interactions, create quantitative atlases of cell activity, and beyond. Illumina offers sequencing platforms and software analysis tools that integrate with partnered solutions to provide a seamless, end-to-end spatial transcriptomics solution with reliability, scalability, and sensitivity.

How Does Spatial Transcriptomics Work?

To spatially resolve mRNA expression in tissue sections, transcripts from sectioned frozen or formalin-fixed, paraffin-embedded tissues are either captured on slides using spatially localized probes or are detected directly in specific regions of interest using photoactive in-situ hybridization probes. cDNA libraries are sequenced and analyzed to quantify expression levels. Depending on the method of choice, expression of 1,200–21,000 protein-coding genes can be quantitatively analyzed in a single readout and accurately mapped to provide transcriptional information on tissue sections.

Transcriptional Profiling of Tissue Sections

Leverage Visium Spatial Gene Expression from 10x Genomics for transcriptional profiling of entire tissue sections.

The Power of Multiomics

Download our in-depth eBook on how multiomic methods have revolutionized research through cutting-edge sequencing and array technology.

A Multiomic Approach to Spatial Biology

Spatial biology can incorporate other analytical methods such as epigenomic, genomic, and proteomic information at the cellular level while similarly providing contextual information within preserved tissues. These methods collectively fall under the term spatial multiomics and offer a multidimensional approach to comprehensively understand biological systems. For many spatial multiomic applications, Illumina offers NGS-powered technologies that can link structural, functional, and spatial insights to enable your next discoveries.

Research Highlights Using Spatial Transcriptomics

Immunological Atlas

Read how investigators use spatial transcriptomics to create an atlas of developing immune systems in humans.

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Understanding the Tumor Microenvironment

Learn how researchers use spatial transcriptomics in tumors to identify differences in microenvironments, gene expression, and therapeutic responses.

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Spatially Mapping Diverse Tissues

See how scientists discovered the spatial layout of diverse cells in various tissues using spatial transcriptomics.

Read Paper

Spatial Transcriptomics Workflow Overview

From sample to discovery, Illumina instruments offer seamless integration with partnered solutions to a single workflow.

Prepare Samples

Section and prepare fresh frozen or formalin-fixed, paraffin-embedded tissues onto slides.

10x Genomics Visium CytAssist for FFPE Tissues

10x Genomics Visium Spatial Gene Expression for FFPE

Profile and Construct Libraries

Image and construct libraries for sequencing steps.

NanoString GeoMx Protein Assays

NanoString GeoMx Whole Transcriptome Atlas

NanoString GeoMx Digital Spatial Profiler

10x Genomics Visium Spatial Gene Expression

10x Genomics Visium Spatial Proteomics

Sequence

Perform sequencing using Illumina instruments.

NovaSeq 6000 System

NextSeq 1000 or 2000 System

NextSeq 550 System

Analyze

Analyze transcriptional data.

DRAGEN GeoMx NGS Pipeline

10x Genomics Space Ranger

Visualize

Visualize and map gene expression to tissue location.

DRAGEN GeoMx NGS Pipeline

10x Genomics Loupe Browser

Highlighted Solutions

Sequencing Instruments

Compare Illumina sequencing instruments by application, throughput, and other key specifications, and determine which platform is right for your needs.

FFPE RNA-Seq From Degraded Tissues

Get high-quality results from formalin-fixed, paraffin-embedded (FFPE) tissues using Illumina RNA-Seq solutions.

Spatial Proteomic and Proteogenomic Insights

Combine the spatial analyses of RNA and protein using the Nanostring GeoMx DSP and Illumina sequencing to understand the heterogeneous pathology of human astrocytoma and glioblastoma samples.

Featured Webinars

Resolving Dynamic Microenvironments in Cancer Research

Learn how NGS-based solutions and NanoString’s GeoMx assays deliver deep insights into tumors and microenvironments.

Building a Tumor Immune Atlas

Watch how researchers link tissue morphology and biological activity to create a reference atlas for tumor pathology.

Spatial Resolution of the Developing Human Cortex

See how scientists are using 10x technologies, single-cell RNA-Seq, and Visium with Illumina sequencing to reveal the spatial resolution of the developing human fetal cortex.

Advances in Spatial Biology and Cancer Research

Scientific experts highlight the historic journey of cancer research using solutions from NanoString and Illumina from a spatial biology perspective.

Spatiotemporal Changes in Cardiac Tissue

Learn about transcriptional changes in different regions of cardiac tissue during early-onset acute myocardial infarction.

Single-Cell Transcriptomic Landscape in Alzheimer’s

See how Dr. Vivek Swarup’s application of spatial transcriptomics has led to advancements in understanding late-stage Alzheimer’s diease.

Customer Stories and Resources

Visualizing Cell Interactions

Read how researchers used spatial insights to add another dimension to their single-cell transcriptomic data.

Understanding the Tumor Microenvironment

Read how the tumor microenvironment can provide essential clues about the behavior of diseased cells.

Precision Immunotherapies

Read how a three-pronged analytical approach is helping researchers identify promising immune targets for cancer immunotherapies.

Sequencing-Based Spatial Genomic Analysis

Learn how spatial multiomic profiling can provide unprecedented molecular information in cancer biopsy samples.

Future of Multiomic Research

Read how spatial information is providing next-generation improvements in multiomic data for cancer research.

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Spatial Transcriptomics

Introduction to Spatial Transcriptomics

Spatially resolve transcriptional activity in complex tissue architectures

What is Spatial Transcriptomics?

Spatial Transcriptomics of Complex Tissues

Benefits of Spatial Transcriptomics

How Does Spatial Transcriptomics Work?

Transcriptional Profiling of Tissue Sections

The Power of Multiomics

A Multiomic Approach to Spatial Biology

Research Highlights Using Spatial Transcriptomics

Immunological Atlas

Understanding the Tumor Microenvironment

Spatially Mapping Diverse Tissues

Spatial Transcriptomics Workflow Overview

From sample to discovery, Illumina instruments offer seamless integration with partnered solutions to a single workflow.

Prepare Samples