Spatial Transcriptomics Services
Utilize 10x Genomics Visium CytAssist to generate high-resolution spatial gene expression profiles from FFPE or fresh-frozen sections, enabling detailed characterization of tumor microenvironments, neural circuits, and immune microenvironments.
Why Spatial Transcriptomics Matters
Spatial transcriptomics merges spatial gene expression profiling with intact tissue architecture, preserving microanatomical detail and capturing mRNA in situ for comprehensive transcriptome mapping. Using the 10x Genomics Visium CytAssist spatial platform, our high-throughput spatial transcriptomic analysis supports both FFPE spatial transcriptomics and fresh-frozen spatial profiling, delivering spatially resolved transcriptomics data across entire tissue sections.
This approach complements bulk RNA-seq, which measures average expression across all cells, and single-cell RNA-seq, which resolves cellular heterogeneity but requires tissue dissociation, by retaining the exact location of each transcript for accurate in situ analysis.
- Map tumor microenvironment interactions with spatial gene expression profiling to uncover immune exclusion patterns and stromal signaling
- Characterize neural circuit transcriptional programs by identifying cell-type-specific gene signatures in defined brain regions.
- Profile inflammatory cytokine landscapes through spatial transcriptomic immune profiling in diseased or inflamed tissues.
- Correlate histopathology with molecular data by overlaying transcriptomic maps on H&E or immunofluorescence images for integrated histology and gene expression analysis.
Spatial Transcriptomic Platforms
Signios Bio uses the 10x Genomics Xenium and Visium CytAssist spatial platforms for high-resolution spatial gene expression profiling of FFPE, fixed frozen or fresh-frozen tissue sections. CytAssist automates probe transfer and library preparation to ensure consistent capture performance and robust gene detection.
| Service | Capture Areas | Species | Resolution | Sample Type | Ideal Application |
|---|---|---|---|---|---|
| Visium HD Service for single cell spatial resolution analysis (probe based) |
6.5 mm × 6.5 mm (2 per slide) |
Human and Mouse | Single cell resolution from continuous lawn of oligonucleotides in a grid of 2 µm barcoded squares – no gaps | FFPE, fresh frozen, and fixed frozen tissue | Near single-cell mapping using Probe-based chemistry. Customize spike in probes to look at viruses or additional genes of interest |
| Visium 3’ HD Service for single cell spatial resolution analysis (poly(A) capture) | 6.5 mm × 6.5 mm (2 per slide) | Any | Single-cell resolution from continuous lawn of oligonucleotides in a grid of 2 µm barcoded squares – no gaps | Fresh frozen tissues | Near single-cell mapping using poly A based capture. Great for discovering novel genes of interest |
| Visium Standard Service for spot based analysis | 11 mm × 11 mm (2 per slide) | Any | 55 µm spot based capture – resolution of 1-10 cells per spot – 100µm gaps between spots | FFPE and fixed frozen tissue | Ideal for capturing spatial heterogeneity in large tissue specimens |
Interested in 10x Xenium services? Contact our scientific team to discuss and optimize your study using standard or customized gene panels.
Full-Service Workflow
Signios Bio offers a turnkey spatial sequencing service, managing every step of your spatial transcriptomics workflow to deliver publication-ready data on a rapid timeline.
- Sample Intake & Quality Control: accept FFPE, fresh-frozen or fixed-frozen tissue blocks or slides; evaluate tissue integrity and RNA quality before proceeding
- Tissue Sectioning & Staining: cryo- or paraffin sectioning to 5–10 µm; optional H&E or multiplex immunofluorescence staining to link morphology with gene expression
- Automated Probe Transfer & Library Preparation: use 10x Genomics Visium CytAssist for precise deposition of barcoded capture probes and streamlined library construction, ensuring consistent spot-to-spot performance
- High-Throughput Sequencing: perform paired-end sequencing on Illumina platforms for robust spatial gene expression coverage
- Bioinformatics Pipeline: run Space Ranger for alignment, spot calling and initial clustering; apply advanced filtering and interactome analysis for deeper insights
- Data Visualization & Delivery: explore results via our MAnGO interactive portal; receive publication-ready spatial feature plots, heatmaps and cluster maps
This comprehensive spatial transcriptomic analysis workflow combines expert tissue handling, automated Visium CytAssist processing, and advanced bioinformatics to reveal gene expression in situ, where it matters.
Determining the Spatial Localization of mRNA Transcripts
Our comprehensive suite of spatial analysis options, ranging from standard analysis to specialized annotation and pathway analysis, gives you a streamlined pathway to unlocking the rich biological insights hidden within spatial data.
- Cluster analysis and spatial plots.
- Advanced filtering for rRNA, mitoRNA, and others.
- Spatial plots showing localization of individual clusters.
- Cell type annotation with spatial context.
- Spatial visualization of interactome.
Applications Across Disciplines
Spatial transcriptomics offers versatile insights across a range of research areas by combining high-resolution gene expression profiling with preserved tissue architecture:
Disease Area
Application
Disease Area
Oncology
Application
Uncover tumor heterogeneity, localize immune cell infiltration zones, and identify stromal interactions to guide the development of targeted therapies
Disease Area
Neuroscience
Application
Map transcriptional programs within precise brain subregions to study neural circuit function and neurological disease mechanisms
Disease Area
Immunology
Application
Profiling spatial cytokine and chemokine landscapes in lymphoid or inflamed tissues reveals immune microenvironment dynamics
Disease Area
Developmental Biology
Application
Visualize gene expression waves during embryogenesis and organogenesis to gain insights into tissue patterning
Disease Area
Regenerative Medicine & Tissue Engineering
Application
Characterize native tissue architecture to inform scaffold design and cell-based therapies
Disease Area
Inflammatory Disease
Application
Differentiate active versus quiescent zones in fibrotic or inflammatory lesions to pinpoint pathogenic niches
This broad applicability makes spatial transcriptomic analysis a powerful tool for academic researchers and biotech teams seeking to link molecular insights with histological context.
Resources & Insights
White Paper
A concise overview of spatial transcriptomics and its key applications in developmental biology, neuroscience, cancer research, and regenerative medicine.
Case Study & On-Demand Webinar
A detailed case study with Dr. Mukesh Nyati of the University of Michigan, plus an in-depth, on-demand webinar examining spatial transcriptomic analysis of lung tumors.
Webinar
Explore altered gene expression in a TBI murine model with Professor Michelle H. Theus of Virginia Tech, Dr. Caroline De Jager, and Marco Corbo, including sample-prep tips, data-integration approaches, and key biological insights.
Why Researchers Choose Signios Bio
Signios Bio stands out as a trusted spatial transcriptomics service provider, offering:
- End-to-end support, from initial consultation through data interpretation, so you never worry about handoffs or delays
- Secure, fast data pipeline, with HIPAA-compatible workflows, encrypted file transfer, and rapid deliverables to protect sensitive samples and meet tight timelines
- Flexible reagent sourcing, use your own 10x Genomics Visium CytAssist kits, or let us procure and manage supplies for you
- Expert bioinformatics analysis, integrating spatial transcriptomics with scRNA-seq or immune profiling to deliver tailored, publication-ready insights
- Interactive visualization portal, MAnGO for exploring spatial feature plots, heatmaps, and cluster maps, plus publication-quality figures included in every report
- Rapid turnaround, complete spatial transcriptomics projects in 2–4 weeks, or opt for data-only analysis in as little as one week
Ready to Start your Next Project with Signios?
Talk to our experts for a tailored spatial transcriptomics quote