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Visium CytAssist (10X Genomics)

Visium Cytassist (10X genomics)

HOW DOES IT WORK?

Visium is a spatial transcriptomics assay that captures gene expression across tissue sections using slides coated with spatially barcoded probes. After tissue permeabilisation, mRNA binds to these probes, which record both the transcript sequence and its spatial location. The assay includes two workflows: a fresh-frozen method where mRNA is captured directly, and a chemistry optimized for both fresh and FFPE tissue, in which paired probes first recognise and ligate onto target transcripts before capture to improve performance with degraded RNA. Visium HD uses this same probe-based chemistry but dramatically increases spatial resolution by reducing capture feature size from 55μm to 2μm. Following library preparation and sequencing, both assays generate spatially resolved gene expression maps, with Visium HD enabling near-single-cell analysis due to its high-density array.

VisiumCytassisthowdoesitwork.png

Source: 10X Genomics

VisiumCytassistmoredetailhowdoesitwork.png

VisiumCytassistworking.png

Source: 10X Genomics

Accessible version

APPLICATIONS
  • Whole Transcriptome gene expression

COMPATIBLE SPECIES
  • Human
  • Mouse

SAMPLE COMPATIBILITY
  • FFPE
  • Fresh Frozen
  • Fixed Frozen

ASSAY INPUT

  • Tissues sectioned onto glass slides

RUN TIME
  • 3 days

ANALYTICAL REGION
  • 6.5mm × 6.5mm per area
  • 2 areas per slide

SINGLE-CELL SCALE RESOLUTION
  •  Transcripts assigned to 2μm square spots, no gaps, for Visium HD assay

CELL SEGMENTATION
  •   From H&E or immunofluorescence imaging

DETECTABLE GENES

Probe-based or oligo dT assay available: 

  • HD WT Panel Gene Expression = Probe-based spatial gene expression assay for comprehensive differential gene expression at single-cell scale. 

  • v2 WT Panel Gene Expression = Probe-based spatial gene expression assay utilising first-generation slide architecture with a large Capture Area option. 

  • HD 3’ Gene Expression = Species agnostic 3’ poly(A) capture-based spatial gene expression assay for expanded whole transcriptome discovery applications. 

  • v1 3’ Gene Expression = 3’ poly(A) capture-based spatial gene expression assay utilising first-generation slide architecture.

Please refer to 10X Genomics’ webpage for product range.