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The High-Throughput Genomics Shared Resource supports the Visium and Visium HD CytAssist Spatial Gene Expression Analysis platforms that were built on probe-based chemistry by 10x Genomics. These CytAssist-enabled platforms facilitate the analysis of whole transcriptome gene expression while maintaining the spatial context of tissue sections. Each Visium or Visium HD CytAssist Spatial Gene Expression Slide contains two Capture Areas that were engineered with spatial barcoded oligonucleotides to capture probes specifically against all known human or mouse genes, respectively. The resulting barcoded sequencing library can be sequenced on an Illumina sequencer and aligned to specific locations of the tissue section based on the barcoded reads.

Differences between Visium CytAssist and Visium HD CytAssist Spatial Gene Expression Analysis

Visium CytAssist Spatial Gene Expression Slide contains two Capture Areas in either 6.5 x 6.5 mm or 11 x 11 mm measurements, providing up to 5,000 or 14,000 barcoded circle spots, respectively, with 50 µm diameter per spot, and 100 µm center-to-center distance between two adjacent spots. The Visium HD CytAssist Spatial Gene Expression Slide contains two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides organized into 11,000,000 features of 2 x 2 µm barcoded square without gaps, ultimately providing single cell-scale resolution.

Visium or Visium HD slide is for single use.  Both Capture Areas of a slide must be used simultaneously. Otherwise, the unused Capture Area will be discarded.

Species Compatibility

The species supported by Visium and Visium HD CytAssist Gene Expression Analysis platforms are human and mouse.

Tissue Compatibility

Visium CytAssist Spatial Gene Expression Analysis platform is designed to analyze gene expression levels in tissue sections derived from formalin fixed & paraffin embedded (FFPE), fresh frozen (FF), or fixed frozen (FxF) embedded tissue blocks. Visium HD platform supports FFPE tissue sections only.

Visium and Visium HD CytAssist Spatial Gene Expression platforms also support archived tissue slides.

RNA Quality Assessment

RNA quality of tissue blocks must be assessed before proceeding with tissue sectioning. 10x Genomics recommends that the percentage of RNA fragments above 200 bp (DV200) is greater than 30% of total RNA.

Timeline

Visium projects require timely coordination with other facilities, such as the ARUP Research Histology Core Facility, the Molecular Diagnostics Shared Resource, and the HSC Cell Imaging Core Facility, all of which impact the length of the project. The following diagram provides estimated timelines with multiple core facilities involved:

Diagram of estimated timelines for Visium CytAssist Workflow, coordinated by multiple core facilities. Step 1: Select right assay. Step 2: Slide preparation and tissue imaging. Step 3: Probe hybridization and transfer to Visium CytAssist. Step 4: Library construction and Illumina sequencing. Step 5: Analysis and discover. Steps 0-4 will take 6-11 weeks. Steps 2b-4 overlap with the first timeline and will take 3-5 weeks.

Data Analysis

A data analysis consultation meeting can be scheduled with Chris Stubben from the HCI Cancer Bioinformatics Shared Resource.

Schedule Consultation

A consultation meeting for setting up Visium Projects can be scheduled with Opal Allen at opal.allen@hci.utah.edu or 801-581-6346.

Contact Us

High-Throughput Genomics Director
Brian K. Dalley, PhD

High-Throughput Genomics Associate Director
Opal Allen, PhD

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Governance

HCI Senior Director Oversight
Alana Welm, PhD

Faculty Advisory Committee Chair
Katherine Varley, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Mei Koh, PhD
Philip Moos, PhD
Andrew Post, MD, PhD
Sean Tavtigian, PhD
Joseph Yost, PhD