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Xenium Analyzer (10X Genomics)

Xenium Analyzer and an image it can produce, next to an image of the IDRM building in Oxford

HOW DOES IT WORK?

Xenium uses a barcoded, in situ hybridization-based workflow to detect and localise RNA transcripts within tissue. Gene-specific padlock probes first hybridise to target RNA and are circularised and enzymatically amplified, creating many copies of each barcode for highly sensitive detection. Fluorescent probes then bind to these barcodes and the tissue is imaged. After each imaging round, the fluorophores are removed and replaced, with each cycle using a distinct fluorescent label. The repeating cycles generate a unique optical signature for every target gene, enabling accurate identification and multiplexed measurement of gene expression at sub-cellular resolution, while preserving spatial context. 

XemiumAnalyzerhowdoesitwork.png

Source: 10X Genomics

Accessible version

APPLICATIONS
  • Targeted gene expression (up to 5,000 genes)
  • Multiomic gene and protein expression (up to 480 genes and 27 proteins)

COMPATIBLE SPECIES
  • Human
  • Mouse
  • Additional species with custom panels (depending on workflow)

SAMPLE COMPATIBILITY
  • Fresh Frozen
  • FFPE 
  • Tissue microarray (TMA)

ASSAY INPUT 
  • Tissues sectioned onto glass slides

INSTRUMENT RUN TIME
  •  4 - 6 days

ANALYTICAL REGION
  • 10.45mm x 22.45mm

SUBCELLULAR RESOLUTION
  • <30nm XY localisation, 200nm per-pixel resolution

CELL SEGMENTATION
  • Nuclei + membrane, cytoplasmic RNA/protein

DETECTABLE GENES
  • Ready-to-use panels (ranging from 50 to 5000 genes) currently:

Xenium Prime 5K Human Pan Tissue & Pathways Panel
Xenium Prime 5K Mouse Pan Tissue & Pathways Panel 

  • Custom panels option of up to ~480 genes (tissue panel); or possibility to add on up to 100 custom genes to one of the following pre-designed panel:

Human Immuno-Oncology               Mouse Brain
Human Multi-Tissue and Cancer     Mouse Tissue Atlassing
Human Breast
Human Brain
Human Lung
Human Skin
Human Colon

  • Ability to add T- and B-cell receptors, SNVs, and isoforms with advanced custom design services
  • Add on Xenium Protein subpanels (listed below) for deeper characterisation of the immune and tumour microenvironment. Possibility to multiplex all 6 subpanels below or only run subpanels of interest:

Immune Cell Subpanel A (CD3, CD4, CD8, CD20)
Immune Cell Subpanel B (HLA-DR, CD68, CD11c, CD138)
Immune Cell Subpanel C (Granzyme B, CD163, CD16)
Tumour Subpanel (PanCK, CD31, Beta-catenin, PTEN)
Proliferation & Differentiation Subpanel (CD45RA, CD45RO, PCNA, Ki-67)
Immune Checkpoint Subpanel (PD-1, PD-L1, VISTA, LAG3)

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