Services
Services available in the ASG Core
Select a service category below to learn more.
Visium HD Spatial Gene Expression
The Visium HD Spatial Gene Expression assay is designed to analyze mRNA in tissue sections derived from formalin fixed & paraffin embedded (FFPE), fresh frozen (FF), or fixed frozen (FxF) tissue samples. Human or mouse whole transcriptome probe panels for each targeted gene are added to the tissue-containing slides, enabling hybridization and ligation of each probe pair. Each Visium HD Slide contains Capture Areas with barcoded squares that include oligonucleotides required to capture gene expression probes at 2 micron resolution, providing an effective resolution of 8 micons after merging features. The total tissue capture area is 6.5mm x 6.5mm. Tissue slides and Visium HD Slides are loaded into the Visium CytAssist instrument, where they are brought into proximity with one another. Gene expression probes are released from the tissue upon a CytAssist-Enabled process, facilitating capture by the spatially-barcoded oligonucleotides present on the Visium slide surface. The Visium HD Slide is removed from the Visium CytAssist for downstream library preparation. Gene expression libraries are generated from each tissue section and sequenced. Spatial Barcodes are used to associate the reads back to the tissue section images for spatial mapping of gene expression.
Assay details and technical information:
https://www.10xgenomics.com/support/cytassist-spatial-gene-expression
Whole Transcriptome probe set information:
https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/probe-sets
Example of Data Visualization and Findings:
Xenium In Situ Gene Expression
The Xenium In Situ Gene Expression workflows measure gene expression with high sensitivity and subcellular resolution in fresh frozen and FFPE tissue sections. Using pre-designed or custom probe panels, the platform targets hundreds to thousands of genes across a variety of tissue types. This platform uses imaging to detect and decode optical signatures at single cell resolution, eliminating the need for sequencing. The total area is 10.5 x 22.5mm to image tissue sections on the slide. The total number of probes that can be used in one experiment include the 5K Xenium Prime pre-designed panel for human or mouse, to which 100 custom genes can be added if needed. Additionally there are a number of pre-designed panels of 200-400 gene targets for mouse, immune-oncology and many other tissues types, to which 100 custom genes can be added.
How it works:
https://www.10xgenomics.com/in-situ-technology
Tissue sections processed using the Xenium In Situ workflow remain largely intact post-run and can be used for additional applications including: immunofluorescence (IF) staining, H&E staining, and whole transcriptome spatial RNA sequencing using the Visium CytAssist Spatial Gene Expression (Visium v2) or Visium HD Spatial Gene Expression (Visium HD) workflows.
Assay details and technical information:
https://www.10xgenomics.com/support/in-situ-gene-expression
Example of Data Visualization and Findings:
Assay Comparison Guide: Visium HD vs. Xenium
Assay | Visium HD | Xenium |
---|---|---|
Compatibility | Fresh Frozen Fixed Frozen FFPE Human & Mouse |
Fresh Frozen FFPE Human & Mouse |
Slide Requirements | Two tissue slides required for each Visium HD Slide run | Two Xenium slides required for each instrument run |
Analyzable Area | Tissue Capture Area per slide: Total Area per run: |
Tissue Capture Area per slide: Total Area per run: |
Workflow options | Pre-run: H&E or IF |
Post-run: H&E, IF, Visium HD, or Visium V2 |
Resolution | 2µm squares - capture area is a continuous lawn of oligos Third Party Software is needed for cell segmentation and deconvolution tools |
Cell segmentation is used to assign transcripts detected in situ |
Target Detection | Whole Transcriptome Probes Spike-in probes can be used (~100s range) |
Probe panels offered: Pre-designed (5k, breast, brain, lung, skin, etc.), add-on custom and stand alone custom |
Assay Advantage | For an unbiased approach. Greater number of transcripts can be detected by increasing sequencing depth. | Increased sensitivity to rare or low-expressing transcripts. |
Workflow | ~3 days From sectioning to sequencing |
~4 days From sectioning to instrument Instrument run length depend on panel size (2-5days) |
Additional services
Next-Generation Sequencing
• Nextseq2000 (Illumina)
Next-Generation Sequencing Via the Advanced Technology Genomics Core (ATGC)
• NovaSeq6000 (Illumina)
• NovaSeqX (Illumina)
Most sequencing services are performed through the Advanced Technology Genomics Core (ATGC) facility, and data is returned to SCGC.