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SPATIAL TRANSCRIPTOMICS

The SCSG Facility provides a comprehensive suite of spatial transcriptomics technologies for mapping gene and protein expression in situ. These approaches integrate molecular data with spatial context, enabling deeper understanding of tissue architecture and cellular interactions. The SCSG Facility is part of a Spatial Transcriptomics collaboration between the Kennedy Institute and the Institute of Developmental and Regenerative Medicine (IDRM), providing access to complementary systems housed at the IDRM.

Spatial Transcriptomics Platforms and Capabilities

CosMx Spatial Molecular Imager (Bruker)

CosMx Spatial Molecular Imager (2).png
  • Imaging-based platform
  • Single-cell and subcellular resolution
  • Whole transcriptome and various targeted panels available for human and mouse tissues
  • Spatial Multiomics gene and protein expression
Find out more about the CosMx SMI

GeoMx Digital Spatial Profiler (Bruker)

GeoMx Digital Spatial Profiler (Bruker).png

  • Sequencing-based platform for Regions of Interest (ROIs)

  • Transcriptome-wide and/or targeted spatial analysis

  • Compatible with human, mouse and canine tissues

  • Spatial Multiomics with whole transcriptome and 570 proteins or TCR profiling

Find out more about the GeoMx DSP

Xenium Analyzer (10X Genomics)

Xenium Analyze (10X Genomics)

  • Imaging-based platform

  • Single-cell and subcellular resolution

  • Targeted single-cell spatial discovery (with up to 5000 gene panels for human and mouse tissues)

  • Spatial Multiomics gene and protein expression (with up to 480 genes and 27 proteins)

  • Hosted at the IDRM (Issa Group) and accessed by KIR researchers with support from the SCSG Facility team

Find out more about the Xenium Analyzer

Visium HD (10X Genomics)

Visium HD (10X Genomics)

  • Single-cell resolution whole transcriptome profiling of human and mouse tissues

  • Probe-based gene expression assays compatible with FFPE, Fresh Frozen and Fixed Frozen tissue sections

  • Poly-A based gene expression assay compatible with Fresh Frozen tissue sections (HD 3’)

Find out more about our Visium CytAssist instrument

Summary

The table below summarises the spatial transcriptomics platforms offered by our facility, allowing for quick comparison of their capabilities.

CosMx (Bruker)

Xenium (10X Genomics)

Visium HD (10X Genomics)

GeoMx (Bruker)

Category

Imaging-based

Imaging-based

Sequencing-based

Sequencing-based

Detectable genes

1000 (1K universal panel),

6000 (6K panel),

Whole Transcriptome

~480 (tissue panel),

5000 (5K-plex panel)

Whole Transcriptome

(probe + oligo dT)

Whole Transcriptome

(probe)

Analytical region

15mm × 20mm / (0.51mm × 0.51mm/FOV)

10.45mm × 22.45mm

6.5mm × 6.5mm / area

(2 areas/slide)

14.1mm × 35.3mm

Resolution

<50nm XY plane

<30nm XY localization,

200nm per-pixel resolution

2μm2 spot, no gaps

100μm2 region

Staining for cell segmentation

Nuclei, membrane,

morphology marker proteins

Nuclei (+ membrane,

cytoplasmic RNA/protein)

H&E/ IF imaging

Nuclei, up to 4 tested

antibodies of choice