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10x Xenium - In Situ Molecular Imaging​

Single cell spatial multiomics​​

Xenium in-situ molecular imaging by Propath

Empowering discovery through
spatially resolved multi-omics​

High-plex in situ multiomics at subcellular resolution provides scalable cell atlas and spatial insights with a comprehensive selection of targeted, customisable panels.

  • Explore the cell atlas, cell-cell interactions and phenotypes of the tissue microenvironment
  • Use curated tissue specific panels, customise them or create fully bespoke signature assays
  • ​End-to-end service from panel design and tissue preparation to data analysis and reporting
Spatially resolved transcriptomics imagery
Cell segmentation in human FFPE lung
Lab technician reviewing cell
Cell classification in whole mouse brain (coronal section)

Xenium at a glance

  • Discovery to signature
    With pre-developed, customisable panels from 250 to 5000 genes​
  • Same slide multi-omics​
    Quantify RNA and Protein expression in a single assay
  • Customisable​
    Fully bespoke panels up to 480 genes, or spike-in to existing panels​​
  • Any species​
    Pre-developed panels available for human and mouse, spike in xenograft donor or microbial targets or build de novo panels for any species ​​
  • Complete service​​​
    From sample prep to data analysis and orthogonal assays​

How the Xenium works​

Sample prep
Imaging
Data processing
Data analysis
Tissue preparation
Target detection
Cyclic imaging
Target decoding
Cell segmentation
RNA & Protein quantification
Cell typing
Data analysis & reporting

Double padlock probes

Dual-recognition and ligation-gated chemistry provides high specificity, minimising off-target amplification, increasing the signal to noise and enabling detection of SNPs, fusion transcripts and splice variants.

Short recognition sites provide robust performance in low quality RNA in FFPE embedded samples. Panels of probes can be designed for tissue, pathway and species specific studies with spatial context.

Dual recognition​
Probe ligation​
Rolling circle amplification​
Fluorescent probe hybridisation​

How researches are using the Xenium

  • ‌Cell atlas and characterisation
    Defining cell types, cell states, tissue microenvironment phenotypes, and gene expression networks within spatial context
  • Cell-cell interaction
    Understanding biological process controlled by ligand-receptor interactions
  • ‌Treatment effects
    Quantifying changes in gene expression before and after treatment
  • ‌Spatial biomarkers
    ‌Identifying single-cell subcellular biomarkers with spatial context
  • Train AI Models
    Automate annotation of cell types for training models on same-section IHC or H&E

‌Propath’s complete service for Xenium studies

We take care of the complete process from sample preparation to data analysis, with robust QA procedures and complete traceability of your precious samples.

Propath responsive support

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Tell us about your study

We’ll explain the complete process and provide as much support as needed to help you make key decisions and generate meaningful data that achieves your objectives.
Select your panel at Propath

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Select your panel and number of Fields of View (FOVs)

Choose from one of NanoString’s validated protein or RNA panels, with the option to spike-in additional protein targets if required.
Defining target areas on samples at Propath

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Sample prep and hybridisation

We prepare your FFPE or fresh frozen samples ready for flow cell analysis, including hybridization of RNA specific probes and antibodies; and assembly of the CosMx flow cell.

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Xenium imaging

Our experienced staff run Xenium analysis within our dedicated spatial lab based in the UK.
Communication and Quality Assurance at Propath

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Communication and QA

Expect regular updates and as many collaborative discussions throughout your study as required.  All our processes are supported by SOPs, traning and QA oversight, developed and refined over 30 years.
Analyse spatial expression on samples at Propath

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AI powered data analysis

We offer a comprehensive, service for data analysis and visualisations, powered by AI, hosted in the cloud and brilliant for collaboration across teams!

Xenium panels

Propath offers pre-developed panels for a range of tissues and can support the design of panel spike in or full panel customisation to ensure sufficient coverage of the target biological systems and intended bioinformatic analyses.​

Focus panels can accommodate up to 480 RNA targets and can include a panel of up to 27 protein targets.

<480 Focus panels - human​

  • Immuno-oncology – 380 genes
    ​Immune cell typing and checkpoint markers
  • Multi-tissue – 377 genes
    For multi-tissue TMAs including heart, pancreas, kidney, liver, skin, lymph etc
  • ​Breast – 280 Genes
    Glandular cells, epithelial cells, adipocytes, tumour etc
  • Brain – 266 Genes​
    Astrocytes, microglia, glioblastoma, Alzheimer’s, Parkinson’s etc
  • Lung – 289 Genes
    ​Alveolar cells, ciliated cells, endothelial cells, respiratory viruses
  • Skin – 260 Genes
    ​Keratinocytes, melanocytes, endothelium, immune cells, melanoma etc
  • ​Colon – 322 Genes
    ​Enterocytes, endocrine cells, goblet cells, paneth cells, fibroblasts etc

<480 Focus panels - mouse​

  • Brain – 247 genes​
    Astrocytes, interneurons, microglia, oligodendrocytes etc
  • Tissue Atlas – 379 genes​
    Multi organ panel for whole mouse imaging​​

<480 Focus panels - mouse​

High-plex discovery panel covering a broad range of tissue types, indications, biological pathways, receptor-ligand pairs to support hypothesis generation, focus panel design and endless reanalysis.
  • 5006 Genes
  • Up to 100 add-in genes
  • Pre-developed core data analysis

5k prime panel - mouse​

High-plex discovery panel covering a broad range of tissue types, indications, biological pathways, receptor-ligand pairs and other​​
  • ​5006 Genes​​​​
  • Up to 100 add-in genes
  • ​​​​Pre-developed core data analysis

Focus protein subpanels​

  • Immune cell subpanel
    CD3 | CD4 | CD8 | CD20
  • Immune cell subpanel
    ​HLA-DR | CD68 | CD11c | CD138
  • ​Immune cell subpanel
    GZMB | CD163 | CD16​​
  • ​Immune checkpoint subpanel
    PD-1 | PD-L1 | VISTA | LAG3​
  • ​Tumour subpanel​
    PanCK | CD31 | Beta-catenin | PTEN
  • Proliferation and differentiation subpanel
    ​CD45RA | CD45RO | PCNA | Ki-67
  • Cell segmentation subpanel
    ​E-cadherin | Vimentin | ɑSMA | CD45

FAQs

Advanced platforms for spatial biology available today at Propath

‌Our experience across a range of platforms for spatial biology allows us to recommend the most appropriate platform for each research project.

We understand the strengths and limitations of each platform – and how to get the best out of them.

Xenium
Targeted, scalable spatial transcriptomics and multi-omics panels at subcellular resolution
‌Validated for GCP studies
PhenoCycler and PhenoImager
High-plex and focussed mIF panels supporting discovery and translational studies
‌Validated for GCP studies
Proximity Ligation Assays
Automated PLA assays for the detection of protein-protein interactions and post- translational modifications​
‌Validated for GCP studies
nCounter, GeoMx and Cosmx
Integrated spatial multi-omics including up to whole transcriptome profiling from tissue to sub-cellular resolution
‌Validated for GCP studies
PhenoCycler and PhenoImager
High plex single-cell spatial phenotyping; and focused mIF panels for high-throughput translational research
‌Validated for GCP studies
COMET
Highly multiplexed sequential immunofluorescence for up to 40 protein on a single slide
‌Validated for GCP studies
nCounter, GeoMx and Cosmx
Integrated spatial multi-omics including up to whole transcriptome profiling from tissue to sub-cellular resolution
‌Validated for GCP studies
RNAscope and COMET
High-plex and focussed multi-omic mIF panels supporting discovery and translational studies
‌Validated for GCP studies
RNAScope and BaseScope
Robust in situ hybridization technology for rapid quantification of any RNA target in any tissue with spatial context
‌Validated for GCP studies

A selection of Propath's work

isPLA analysis highlighting receptor-ligand binding in pink, interacting cells in red and non-interacting cells in blue
AI guided spatial transcriptomics analysis investigating role of hypoxia in immune cell exclusion in head and neck cancer
Artefact detection demonstrating exclusion of erythrocytes while retaining lower signal from fluor labelled antibody
AAV distribution analysis including glomerulus detection, cell segmentation and classification with RNAscope quantification
Bespoke sensory neuron and satellite cell segmentation for in-situ gene expression assay by CosMx in dorsal root ganglion
Spatial plot representing immune cell phenotypes assigned from a mIF stain generated by COMET on atopic dermatitis

A selection of our work

Outsourced R&D - Done better.

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