Single Cell & Spatial Multiomics

The Monash Genomics & Bioinformatics Platform offers comprehensive 10x Genomics technologies for single cell and spatial analysis. Our capabilities include the Chromium X for high-throughput single cell multiomics, the Visium CytAssist for spatial transcriptomics on tissue sections, and the Xenium Analyzer for high-resolution in situ transcriptomics. Together, these technologies enable deep cellular and spatial insights across diverse biological systems.

Single Cell Applications

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  • 🧫 Single Cell Gene Expression

    3′ or 5′ assays for single-cell transcriptomes

  • 🧠 Immune Profiling (VDJ)

    Combined TCR/BCR VDJ and gene expression profiling

  • 🧬 Multiome (ATAC + RNA)

    Joint chromatin accessibility and transcriptional profiling from the same cells

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  • 🧩 Feature Barcoding

    Detection of cell surface proteins or CRISPR guides

  • 🧪 Sample Multiplexing

    Pooling multiple samples using TotalSeq hashing antibodies

Spatial Multiomics Applications

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  • 🧬 Visium HD Whole Transcriptome

    Probe-based whole-transcriptome spatial mapping for human and mouse tissue, delivering subcellular resolution and comprehensive gene coverage.

  • 🌍 Visium HD 3′ Gene Expression

    Poly-A capture-based spatial gene expression profiling for species without predefined probe panels, enabling flexible applications beyond human and mouse.

  • 🔬 Xenium In Situ Analysis

    High-plex RNA and protein detection at subcellular resolution for detailed in situ characterisation of tissue architecture and cell-cell interactions.

Instrumentation

The 10x Genomics Chromium X is a high-throughput microfluidics platform for single-cell and single-nucleus analysis. It partitions and barcodes individual cells or nuclei into nanolitre-scale Gel Beads-in-Emulsion (GEMs), enabling capture of hundreds of thousands to over a million cells per run. Compatible with a wide range of 10x assays—including gene expression, immune profiling, multiome, and ATAC—the Chromium X delivers reproducible, scalable single-cell data with minimal hands-on time and streamlined, one-day workflows.Chromium X
The 10x Genomics Visium CytAssist is a compact benchtop instrument that simplifies and standardises spatial transcriptomics workflows. It enables tissue sectioning, staining, and imaging on standard glass slides, followed by precise transfer of transcriptomic material onto Visium capture areas. Compatible with both fresh-frozen and FFPE samples, the CytAssist improves spatial accuracy, supports a wide range of tissue types, and ensures consistent, high-quality data generation for spatial gene expression studies.10x Genomics Visium CytAssist
The 10x Genomics Xenium is an advanced in situ spatial transcriptomics platform that enables high-plex gene expression profiling at subcellular resolution. It can detect hundreds to thousands of RNA targets directly within intact tissue sections from fresh-frozen or FFPE samples, providing single-cell and subcellular spatial context. Combining precise probe chemistry, automated imaging, and powerful data visualisation, Xenium reveals detailed tissue architecture, cell–cell interactions, and gene expression patterns with exceptional accuracy and reproducibility.10x Genomics Xenium Analyzer

How To Use Our Single Cell and Spatial Multiomics Services

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  • Discovery

    Contact our team to discuss your research goals, experimental design, and the most appropriate single-cell or spatial workflow for your samples. We can advise on assay selection, input requirements, and expected outcomes. If required, we will also loop in the Monash Histology Platform.

  • Quote

    Once project details are confirmed, we’ll provide a detailed quote outlining costs, timelines, and deliverables.

  • Submit Your Samples

    We will advise the optimal conditions, format, and timing for sample delivery to ensure the highest quality results. Our staff can assist with any required pre-submission QC or preparation.

  • Data Generation & Analysis

    Your project will be processed using our validated workflows, and results will be delivered securely. We also offer support for downstream data analysis through the Monash Bioinformatics Platform.

Close up of test tube samples

Contact Us

Sanger: sequence@monash.edu

All Other Enquiries: micromongenomics@monash.edu

Phone: 9905 4847 (Sanger) or 9905 5487 (All Other Enquiries)

Address: Building 13D, Level 1, 35 Rainforest Walk, Monash University 3800

Location: Find us on the Monash Digital Wayfinder