Visium Spatial Genomics

Visium spatial gene expression measures total mRNA with morphological context in intact tissue samples, both fresh frozen or FFPE. This can be used to map whole transcriptomes in order to better investigate disease pathology, development, and clinical translational research.

Spatial gene expression slides contain 4 capture areas (6.5 x 6.5mm) bordered by a fiducial frame (8 x 8 mm with the frame). Each capture area contains ~5,000 gene expression “spots”, which in turn contains primers comprised of the following:

  • Illumina TruSeq Read 1
  • 16 nt Spatial Barcode
  • 12 nt unique molecular identifier (UMI)
  • 30 nt poly(dt) sequence (to capture poly-adenylated mRNA for cDNA synthesis)

Consultation and Assistance

Contact for Genomics and Bioinformatics Consultation

Details about sample preparation, requirements, library prep types, prices and application are all listed on this page. For more information and assistance:

  • Yaravi Zuleira Suarez (yzs96757@uga.edu), Genomics Specialist, for technical questions about existing or new Visium projects.
  • Please visit our “All Inquiries” page for detailed information about who you should contact at GGBC to receive a quick and accurate response.

Workflow

10x Visium Spatial Transcriptomics Workflow

Step in WorkflowSummary/Notes10x Guide and LinkCustomer or GGBC10x How-To Videos
Fresh Frozen Tissue Block PreparationTissue block preparation; any block of the same tissue type can be used for TO stepLink to Tissue Prep Guide (refer to pg. 5-9)Completed by customer; protocols for simultaneous or separate embedding/freezingLink to Tissue Preparation Guide Video
RNA Quality Assessment
Sample Collection
Tissue collection from all sample blocks for RNA extractionLink to Tissue Prep Guide (refer to pg. 17-18)Either customer uses cryostat (hourly rate) or GGBC collects with customer present
RNA Quality Assessment RNA ExtractionRNA extraction using Qiagen RNeasy Mini KitLink to Tissue Prep Guide (refer to pg. 17-18)Completed by customer
RNA Quality AssessmentBioanalyzer RunRun RNA on bioanalyzer for RIN scoresLink to Tissue Prep Guide (refer to pg. 17-18)Either by customer or GGBC bioanalyzer order
Tissue Sectioning/Slide Preparation (TO & GE)Tissue permeability time optimizationLink to Tissue Prep Guide (refer to pg. 10-16)Either customer uses cryostat (hourly rate) or GGBC sections & assembles slide
Methanol Fixation, H&E Staining (TO & GE)Tissue fixation & stainingLink to Fixation & Staining ProtocolsCompleted by GGBC
Imaging (TO & GE)EVOS systemLink to Imaging GuidelinesCompleted by GGBC
Tissue Optimization (TO) Slide ProcessingDetermination of permeability timeLink to Tissue Optimization User GuideCompleted by GGBCLink to TO Protocol Video
Gene Expression (GE) Slide ProcessingPermeability Step through Library ConstructionLink to Gene Expression User GuideCompleted by GGBCLink to GE Protocol Video
Pre-Seq QC & SequencingLink to Gene Expression User Guide (pg. 59-61)Completed by GGBC

TO = Tissue Optimization         GE = Gene Expression

 

Helpful Links Related to Visium Spatial Genomics Sample Preparation

Tissue Preparation Guide

Fresh Frozen Tissues Tested

Fresh Frozen How-To-Video

FFPE Tissues Tested

FFPE How-To-Video

 

1. Tissue Permeability Optimization
https://assets.ctfassets.net/an68im79xiti/3jBtg0tFMD28GaEqoStahT/2cc85436f97d5b9192e8201cf4961d88/CG000238_VisiumSpatialTissueOptimizationUserGuide_RevE.pdf

For new projects / new tissue types, tissue permeability optimization will need to be performed. This process ensures the optimal permeabilization time is chosen; this time point should result in maximum fluorescence signal with the lowest signal diffusion. Each tissue type will require its own permeability optimization. Tissue permeability does NOT need to be performed on the specific sample block, but rather the same tissue TYPE. Please clearly label the block(s) and indicate on the order form which block(s) should be utilized for either Gene expression or tissue optimization.

The cryostat at the core can be utilized by researchers for a small fee. Please contact GGBC (ggbc@uga.edu) to schedule this service. The customer may prepare both their tissue optimization slide and gene expression slide simultaneously. The tissue optimization slide will be stored in the -80°C until tissue optimization is complete. Both slides are stable in the -80°C for up to 4 weeks.

 

 

2. Slide Preparation

Tissue Sectioning / Slide Submission
Tissue sectioning can be done by the researcher, or fresh frozen / FFPE blocks can be provided to the core for sectioning.

Slides are stable for up to four weeks in -80°C and can be shipped on dry ice to the GGBC facility.

Gene Expression Slide Specifications

Capture Area TypeSizeBarcoded SpotsSpot Size
Standard6.5mm x 6.5 mm~500055um
XL capture11 mm x 11 mm~14,00055 um

*1-10 cells will cover a spot, depending on the type of tissue used.

H&E Staining and Imaging

Slides are stained using hematoxylin and eosin (H&E) staining and are imaged using EVOS.

3.Permeabilize Gene Expression Tissue and Construct Library

 

 

Prices and Quotes

Contact for Financial Inquiries and Quote Requests

Please email Kim and Elizabeth at ggbc@uga.edu, for financial inquiries or to request a quote. Be as specific as possible, so that they can more quickly assist you.

A Note About Visium Spatial Transcriptomics Projects:

Please contact the core to inquire about pricing. Scheduling projects with other lab groups may be beneficial. If no other group(s) require tissue optimization around the time a customer needs this service, the core may charge the customer for the full price of the kit.

Visium Spatial Transcriptomics

StepServiceUGA FeeNon-UGA FeeCommercial Fee
1. Tissue Permeability OptimizationOne Slide
$1,383.00
$1,632.00
$1,729.00
4 Slides$4,332.00$5,111.00$5,414.00
2. Tissue Sectioning and Slide PreparationIncludes tissues sectioning, staining, and imaging a single slide with up to 4 capture areas.$168.00$199.00$210.00
3. Tissue Gene Expression Library PrepIncludes cDNA synthesis, cDNA QC, library prep, library QC$6,621.00$7,813.00$8,276.00
4. Library PoolingLibrary Pooling$60.00$71.00$75.00
5. Pre-Sequencing QCQC the final library before preparing to load$120.00$142.00$150.00
6. NextSeq 2000 Sequencing RunRun can vary depending on output requirements. Typically P2 or P3.Price will vary based on flow cell.Price will vary based on flow cell.Price will vary based on flow cell.
Cryostat Training1 hour training with designated laboratory personnel. After a customer is “trained” they are free to schedule cryostat use.$50.00$59.00$63.00
Cryostat UseTrained customers are welcome to schedule cryostat usage in increments of 1 hour.$15.00$18.00$19.00

Data Analysis

10X Space Ranger analysis software can be utilized to process spatial gene and/or protein expression data. This software can be utilized in conjunction with Loupe Browser visualization software.

Resources:

https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger [Name “Space Ranger Analysis Pipelines”]

https://support.10xgenomics.com/spatial-gene-expression/software/visualization/latest/what-is-loupe-browser [Name “Loupe Browser Visualization software”]