Spatial Omics Platforms
Spatial transcriptomics is a cutting-edge approach that measures gene expression while preserving the spatial context of cells within a tissue. Unlike single-cell transcriptomics, which requires cells to be dissociated, spatial methods allow researchers to see where genes are expressed within intact tissue architecture. This makes it possible to map molecular activity across brain regions, link gene expression to histological features, and study how cells interact with their neighbors in health and disease.
Currently we offer library preparation services for:
10x Genomics Visium and Visium HD platforms
Compatible with fresh-frozen, fixed frozen, and FFPE tissues.
Probe based whole transcriptome for mouse and human, or species agnostic 3` whole transcriptome.
Bruker CosMX Spatial Molecular Imager
Compatible with Fresh Frozen and FFPE tissues. (Contact us to discuss optimization for fixed frozen tissues)
Panel based or whole transcriptome subcellular spatial transcriptomics to fit the size and budget of your research needs.
Spatial proteomics and same slide multi-omics capabilities offer true spatial multiomic data generation to get the absolute most out of your valuable tissue samples.
Assays coming soon:
Illumina StrataMap Spatial Transcriptome solution
- Instrument free, species agnostic, whole transcriptome, accessible spatial transcriptomics at single cell resolution with the largest available FOV
RNA Extraction and RIN/DV200 assessment
These are correlated with improved assay outcomes but do not guarantee high yields
- For Visium HD on fresh frozen tissue, a minimum RIN value of ≥4 is recommended to improve assay outcomes.
- For Visium HD on fixed frozen tissues, a DV200 value ≥ 50% is recommended to improve assay outcomes.
- For Visium HD on FFPE tissues, a DV200 value ≥ 30% is recommended to improve assay outcomes.
DAPI nuclei morphology assessment
An optional check for the quality of cell nuclei prior to running the assay. DAPI staining is performed to check for:
- Punctate nuclei that are clearly defined
- DAPI staining that does not appear washed out
Slide preparation for assay:
Tissue sectioning from paraffin or frozen blocks for Visium or CosMX assays
- FFPE: 3–10 µm (5 µm recommended)
- Fresh/fixed-frozen: 10–20 µm (10 µm recommended, but up to 20 µm has been validated by 10X for Visium HD)
H&E staining and high resolution 20X tissue imaging (imaging in partnership with HBI AMP Facility)
Paraffin Embedding
Fixed tissues can be provided to the Neuro Omics Core for tissue processing and paraffin embedding services for use in spatial transcriptomic workflows