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URMC / Research / Rochester Genomics Center / Services / Spatial Genomics

Spatial Genomics

Images of Spleen used for 10X Visium Spatial Transcriptomics10X Visium Spatial Gene Expression

Measure gene expression activity in the context of tissue microenvironment. 

H&E and gene clustering image of mouse brain using spatial transcriptomics from 10X Genomics

Visium with H&E: Use H&E staining for morphological context

Immunofluroescent image with cell clusters overlayed from 10X Genomics                     Targeted Gene Expression Image from 10X Genomics

Visium with Immunofluorescence                         Visium with Targeted Gene Expression
Combine Gene Expression with                                 Focus on target genes in pre-designed
Immunofluorescent staining for                                panels, add up to 200 genes to panels,
Spatial Proteomics                                                       or customize your own panel. 


How Does Visium Work?

Visium Spatial Gene Expression slide with 4 capture areas contains barcoded spots with millions of poly-dT oligos to capture mRNA Transcripts from tissue

Gene expression slides contain 4 capture areas (6.5mm x 6.5mm) that each contain 5000 barcoded spots. Each spot contains millions of oligonucleotides with spatially barcoded sequences revealing the location of the mRNA transcripts released from the tissue on the slide. 

How does Visium Work? 

Sample Requirements:

Fresh Frozen Tissue: 

  • Tissue should be snap frozen and embedded in OCT embedding medium. For detailed tissue preparation, please reference the 10X Tissue Preparation Guide
  • Prior to placement on the optimization or gene expression slide, RNA quality should be assessed by collecting 10 (10um) sections for RNA extraction and QC. 10X recommends use of tissue blocks with a RIN value of 7 or greater. 
  • For a list of tested tissues and recommended tissue thickness, please reference the 10X Tested Tissues List
  • Before proceeding with the Gene Expression slide, Tissue Optimization should be completed on each new tissue type. The Optimization slide is used to determine the optimal permeabilization time. This will require 7 tissue sections at the appropriate thickness. 

FFPE Tissue:

  • Compatible with Human and Mouse tissues at 5um. For detailed tissue preparation, please reference the 10X FFPE Tissue Preparation Guide
  • Prior to placement on the slides, RNA quality should be assessed by collecting 2-4 (10um) sections for RNA extraction and QC. 10X recommends use of FFPE tissue blocks with a DV200% of 50% or greater. 
  • Prior to placement of section on the Gene Expression slide, a tissue adhesion test must be completed to confirm tissue will remain attached to the slide during the workflow. This will require 4 sections at 5um. 
  • Probe-based design: ~18,000 Human Gene Targets and ~20,000 Mouse Gene Targets

Visium for Fresh Frozen Overview:

10X Visium Fresh Frozen Workflow including Tissue Preparation, Methanol Fixation and H&E Staining, Tissue Opimization, and Library Construction

Prior to completing a Gene Expression study using Fresh Frozen tissue, a Tissue Optimization experiment must be completed on each new tissue type. This will determine the optimal permeabilization time for the gene expression slide. 

Visium for FFPE Overview:

Visium Spatial FFPE Workflow including Tissue preparation, tissue test slide, and library construction 

Learn more about Visium for FFPE

Learn more about 10X Visium Spatial Gene Expression.

Coordination with GRC:

The GRC usually stocks Tissue Optimization Slides (FF) and Tissue Section Test Slides (FFPE). Due to expiration of reagents, we order Gene Expression Slides and Reagent Kits as needed. If you are in need of sectioning assistance, we have several contacts we can coordinate with for slide transfer and cutting. 

Once tissue sections are placed on the slide, they are stable for up to 4 weeks at -80C. They can then be transported to the Genomics Research Center on dry ice where the GRC staff will complete the remaining workflow components. 

If you would prefer to complete the lab work in your lab, please let us know and we can coordinate transfer of slides and reagents. You can then submit ready-to-sequence libraries to the GRC using our User Prepared Library submission form on our Sample Submission Page


NanoString GeoMx ROI

NanoString GeoMx Spatial Profiling

Compatible with many tissue types: 

NanoString GeoMx Tissue Types

No special slides are required for this platform as long as tissue is placed within the green area shown above. 

Profile Protein with oligo labeled antibodies or RNA with oligo-labeled probes: 

  • Protein: developed Human + Mouse Immunology and Oncology Panels with custom options available through abcam
  • Whole Transcriptome RNA profiling with 18,000+ gene specific probes for human/mouse

How to start a nanostring geomx project with the GRC:

1) We prefer to have meetings with investigators to discuss the steps of the project and ensure this is the correct approach for your research goals. It is critical to meet with the GRC staff to ensure the instrument and necessary reagents are available for your project. Please contact us to schedule a meeting. 

2) Next, identify morphology markers that will help with morphological identification of your tissue of interest and assist with Region of Interest (ROI) selection. NanoString GeoMx has a list of tested markers available here

3) Test the morphology markers on your tissues using the NanoString protocol. This can be done by the lab or by the GRC. You should use tissue blocks that allow for testing or tissue blocks that are comparable to the tissue you would like to use for your experiment. 

4) Scan the test slides to obtain morphology marker stain efficiency and to practice ROI selection to familiarize yourself with the software and better understand the capabilities of the system. 

5) Once the testing phase is complete, proceed with tissue placement and move forward with gene expression or protein experiment. There will be a stage of ROI selection which is time sensitive. We will be sure to coordinate this with the availability of the lab members to ensure ample time to select ROIs. 

For more information about the spatial technologies and how we can support your research goals, please contact us