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Rochester Genomics Center

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 GenomicsVisium with Immunofluorescence                       
Combine Gene Expression with                                 
Immunofluorescent staining for                               
Spatial Proteomics                                                  

 

 

 

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. 
  • Probe-based design: ~18,000 Human Gene Targets and ~20,000 Mouse Gene Targets

Visium HD Now Available! 

 Visium HD slide layout

Explore spatial transcriptomics at single-cell resolution with the Visium HD. 

Learn more about 10X Visium Spatial Gene Expression.

Coordination with GRC:

If you are interested in performing a Visium experiment, please contact us so we can schedule a project consulation. 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 a contact we can coordinate with for slide transfer and cutting. 

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. 

 

Xenium in situ Analyzer

10X Genomics Xenium Analyzer

State-of-the-art single cell spatial imaging platform. Compatible with Fresh Frozen (FF) or FFPE tissues utilzing diverse menu of customizable panels. For more information on available panels, please click here. 

Once tissues sections are placed on the Xenium Slide hand off to the GRC for us to complete processing: 

XeniumWorkflow

Analysis once the imaging is complete: 

XeniumAnalysis

If you are interested in completing a Xenium experiment, please contact us to discuss your project in more detail! 

 

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: 

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

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!