10x Genomics

10x Genomics – Certified Service Provider

We are a certified service provider for 10x Genomics, providing our clients with access to innovative solutions for single-cell assays and spatial genomics, including transcriptomics and chromatin accessibility (ATAC-seq). We are one of the few commercial providers offering all three 10x Genomics spatial omics platforms:

• Xenium – High-Resolution In Situ Spatial Gene Expression Analysis
• Visium – Unbiased Whole Transcriptome Single-Cell Analysis
• Chromium – Single-Cell RNA-Seq and ATAC-Seq

The established Certified Service Provider Program is designed so that clients can access a reliable provider network for outsourcing genomic and single-cell analysis through global service providers.

Fee-for-service laboratories can qualify for inclusion in the program if they meet high technical and service standards. These requirements are reviewed annually for each selected application, which may involve one or more of the 10x Genomics solutions we offer.

Application Areas for the 10x Genomics Solutions include:

• COVID-19
• Infectious Disease
• Immunology
• Oncology
• Neuroscience
• Rare Disease
• Neurodegenerative Disease
• Drug Discovery

The Certified Service Provider partnership with 10x Genomics includes training, evaluation, and an annual recertification process. The certified services include:

Xenium

Visium

• Establish the spatial profiles of entire transcriptomes across complex tissues using species-agnostic analysis of FFPE samples.
• Detect splice variants, SNVs, and gene expression patterns with spatial resolution via next-generation sequencing.
• Combine traditional histology with spatial transcriptomics to identify regional transcriptomic patterns and cellular states.
• Use Visium for discovery-driven projects or to complement focused panels from Xenium to contextualize high-resolution findings.

Chromium X

• Analyze how cellular heterogeneity contributes to your biological system with transcriptional profiling at single-cell resolution across tens of thousands of cells.
• Gain new insights into cell subtypes and states with multiomic readouts of gene and cell surface protein expression.
• Explore cellular phenotypes with whole transcriptome analysis or focus on relevant genes and pathways using pre-designed or custom Targeted Gene Expression panels.
• Investigate complex genetic networks and perturbed transcriptomes in normal and diseased cell types by simultaneously detecting CRISPR guides and single-cell gene expression profiles.
• Achieve consistent workflows with Chromium Connect, an automated platform for single-cell sequencing workflows.

What Do These Workflow Solutions Look Like?

Example of an integrated oncology workflow using 10x Genomics Chromium, Visium, and Xenium.

Step 1: Sample Acquisition and Storage

• Tissue biopsies or resected tumor samples are received through our kitting and logistics services and FFPE-fixed upon arrival.
• Samples are cataloged and securely stored in our ISBER-standard biorepository under appropriate conditions.

Step 2: Initial Whole-Tissue Profiling with Visium

• The client requests spatial transcriptomic profiling of a tumor region of interest. Our histology lab prepares sections from FFPE blocks and performs H&E or IF staining to assess tissue quality.
• Slides are processed by our experts using specialized Visium HD slides to generate whole-transcriptome spatial expression profiles across tumor regions.
• This reveals microenvironmental architecture, transcriptomic hotspots, and intratumoral heterogeneity.

Step 3: Focused High-Resolution Spatial Analysis with Xenium

• Based on Visium results, a specific subregion (e.g., invasive margin, immune-dense region) is selected for deeper analysis.
• Adjacent tissue sections are mounted on Xenium-compatible slides, and the same tissue block is used for continuity.
• Customized or predefined Xenium panels (e.g., immuno-oncology) are used to detect up to 5,000 genes in situ.
• Our experts use the Xenium instrument to capture spatial gene expression data at single-cell and subcellular resolution, allowing visualization of tumor-immune interactions.

Step 4: Single-Cell Transcriptomics and Epigenetics with Chromium

In parallel or as a follow-up, cryopreserved or fresh-dissociated tumor tissue is processed by Sampled’s Cell Lab to generate a single-cell suspension.

Single-cell assays are selected based on research goals:

• scRNA-seq to profile individual tumor and immune cell populations
  
• scATAC-seq to explore chromatin accessibility and regulatory mechanisms

Step 5: Data Analysis and Integration

• Each dataset, spatial (Visium/Xenium) and single-cell (Chromium), is analyzed by Sampled’s bioinformatics team or sent directly to the client for analysis.
• Data is delivered via SampledSphere^®, allowing the client to explore integrated insights or download structured datasets for internal analysis.