Spatial Genomics

Visium Tissue Optimization: $1,580.96/sample

  • This service is a necessary step prior to performing the Visium: Fresh Frozen assay.
  • In collaboration with the Pathology Shared Resource, 7x10um tissue sections are cut onto Visium Tissue Optimization slides and a time course is performed to determine the optimal tissue permeabilization time for the assay.
  • A separate tissue optimization run should be performed for each tissue type to be tested. It is also recommended to separately optimize healthy vs diseased samples, if significant differences in tissue architecture or properties exist.

Visium Fresh Frozen: $6,823.27/sample

  • This service is for the preparation of tissue sections for spatial transcriptomics using the 10x Genomics Visium assay for fresh frozen tissues.
  • In collaboration with the Pathology Shared Resource (PSR), 10um sections are cut and placed directly on the Visium slide (4 capture areas per slide). H&E staining and imaging (20x) are performed in the Single Cell Genomics Core. Transcripts are detected using a PolyA-based approach, making the assay applicable to a wide range of species including human, mouse, rat, zebrafish and more.

Visium FFPE: $9,296.73/sample

  • This service is to perform the 10x Genomics Visium assay on FFPE tissue sections.
  • In collaboration with the Pathology Shared Resource, 5um FFPE sections are cut onto standard histology slides, followed by clinical-grade H&E staining and 40x whole-slide imaging. probes targeting the whole transcriptome are hybridized to the tissue section and transferred to the Visium slide using a 10x Genomics CytAssist to preserve the spatial distribution of the probes.
  • Each Capture Area contains either 5,000 (6.5 x 6.5 mm) or 14,000 (11 x 11 mm) barcoded spots that are 55 µm in diameter (100 µm center to center between spots, providing an average resolution of 1 to 10 cells per spot).

Visium HD: $14,396.73/sample

  • This service is to perform the 10x Genomics Visium HD assay on tissue sections.
  • In collaboration with the Pathology Shared Resource, 5um FFPE sections are cut onto standard histology slides, followed by clinical-grade H&E staining and 40x whole-slide imaging. probes targeting the whole transcriptome are hybridized to the tissue section and transferred to the Visium slide using a 10x Genomics CytAssist to preserve the spatial distribution of the probes (2 capture areas per slide).
  • Visium HD Spatial Gene Expression slides contain two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides arrayed in ~11 million 2 x 2 µm barcoded squares without gaps, achieving single cell–scale spatial resolution.

Xenium Sample Prep: $1,110.64/sample

  • This service is to prepare tissue sections for the 10x Genomics Xenium assay.
  • In collaboration with the Pathology Shared Resource, tissue sections are cut onto Xenium slides, then probes are hybridized and ligated to their targets.  The amplified targets are analyzed to build a spatial map of the transcripts across the tissue section.  Custom or off the shelf probe sets are available from 10X Genomics.

Xenium: $3,766.92/sample

  • This service is to perform the 10x Genomics Xenium assay on tissue sections.
  • In collaboration with the Pathology Shared Resource, tissue sections are cut onto Xenium slides, then probes are hybridized and ligated to their targets.  The amplified targets are analyzed to build a spatial map of the transcripts across the tissue section.  Custom or off the shelf probe sets are available from 10X Genomics.

Prices shown reflect internal Dartmouth rates for FY2025. External users and those with large projects should contact the core directly for pricing information. Actual prices may vary based on batch size.

All services provided by the GMBSR are supported by an NCI Cancer Center Support Grant (5P30CA023108) which MUST be cited in any publications or other materials using data generated in the core.

Single cell sequencing services are provided through the Single Cell Genomics Core and are subsidized by a COBRE grant (P20GM130454). This grant MUST be cited in all publications and materials using single cell data generated in the core.

Genomics Services