Introduction to spatial transcriptomics
Spatial transcriptomics measures gene expression while preserving the location of the signal within a tissue section. The CoLab offers approaches ranging from broad spatial transcriptome discovery to targeted, highly localized in situ RNA measurement.
Spatial transcriptomics is especially useful when tissue architecture is essential to the biological question. For example, to study tissue niches, developmental organization, immune infiltration, tumor margins or the relationship between molecular states and histology. Visium HD is generally considered for broad spatial discovery, while Xenium is considered when targeted single-cell localization is the priority.
Spatial assays may not be necessary when location is unimportant or when dissociated single-cell or bulk measurements answer the question more efficiently. Visium HD analysis bins should not automatically be interpreted as individual cells. Xenium is panel based and cannot measure genes that are not included in the selected panel. Poor tissue morphology, incompatible preservation, low RNA quality, unsuitable section placement, or inadequate panel design can limit results.
Compatible sample types
Compatibility depends on the selected platform, tissue type, species, preservation and embedding method, fixation history, tissue dimensions, section thickness and placement, slide type, morphology, and RNA quality. Fresh-frozen, fixed-frozen, and FFPE workflows may be available in particular assay configurations, but the requirements are not interchangeable. Contact the CoLab before cutting valuable tissue or preparing archival slides.
Genomics CoLab offerings
Visium HD: Sequencing-based spatial gene-expression measurement using a dense array of 2-micrometer barcoded squares. It supports broad spatial discovery and can be analyzed at single-cell scale with image-guided binning or segmentation. The exact 3' capture or probe-based whole-transcriptome workflow is selected based on tissue preservation, species, and discovery needs.
Xenium v1 and 5K: Targeted in situ RNA detection with single-cell and subcellular localization. Legacy panel configurations measure fewer than 500 selected genes; Xenium Prime 5K provides a much broader predefined panel with limited custom
additions, subject to current product and local availability.
See our spatial transcriptomics pricing.
Design considerations
When you start your project you will discuss with Genomics CoLab term the following items to assure we can meet your project needs:
- Broad transcriptome discovery versus targeted localization.
- Tissue type, species, preservation, embedding, fixation, storage, and RNA quality.
- Tissue dimensions, orientation, number of sections, and fit within the capture or imaging area.
- Sectioning, staining, morphology imaging, pathology review, and segmentation responsibilities.
- Biological replication, serial sections, adjacent histology, and regions of interest.
- For Xenium, panel choice, custom genes, expected gene abundance, and markers needed to distinguish closely related cell types.
- For Visium HD, chemistry, sequencing depth, binning strategy, segmentation, and integration with histology or single-cell references.
What the CoLab performs
Depending on the project, the CoLab reviews tissue and assay compatibility, performs the selected spatial workflow, library preparation or in situ processing, imaging, quality control, sequencing coordination, primary platform processing, and agreed analysis. If designing a Xenium custom panel is a bottle neck or challenge, the Genomics CoLab can help. Sectioning, tissue preparation, imaging, panel review, and segmentation may be separate components and should be assigned explicitly.
What the investigator supplies
The investigator supplies tissue blocks, sections or slides; preservation and processing history; sample and pathology metadata; tissue dimensions and orientation; species; biological replicates; regions of interest; and, for targeted assays, a probe panels or data from which a panel can be designed.
Data and analysis delivered
For Xenium, deliverables include imaging data, processed spatial expression matrices, morphology images, tissue and cell-segmentation outputs, spatial quality metrics, gene-expression maps, cell-type or region annotations, and project-specific comparisons. For Visium HD, default data deliverables are raw sequencing and may be expanded to include the space ranger output and downstream analysis comparable to the Xenium outputs.
Pricing and sequencing considerations
Spatial pricing may include sectioning, hybridization, probe panels, imaging, segmentation, library preparation, sequencing, and analysis. Visium HD normally has a material sequencing component; Xenium costs depend strongly on panel, slide, imaging, and segmentation choices.
To start a project
Please download our project description form, fill it in with the as much detail as you can and then send it along with a consultation request to the [email protected] email address.