Skip to main content
Fatty tissue from fresh frozen sample
Helmholtz Munich | @Melisa Gomez Velazquez

Spatial Transcriptomics

Spatial Transcriptomics is a cutting-edge molecular profiling method that allows scientists to measure all the gene activity in a tissue sample and map where the activity is occurring. Defining the spatial distribution of mRNA molecules allows to uncover cellular heterogeneity in tissues, tumours, immune cells as well as determine the subcellular distribution of transcripts in various conditions. This information provides a unique opportunity to decipher both the cellular and subcellular architecture in both tissues and individual cells.

Collaborating seamlessly with CF-PTA (learn more here), CF-Genomics offers sample processing services for spatial transcriptomics, leveraging the revolutionary 10x Genomics Xenium in situ technology. This process involves the hybridization of several hundred probes, subsequently ligated, amplified, and identified through multiple rounds of probe hybridization and removal. This intricate procedure enables the simultaneous analysis of several hundred transcripts, providing unparalleled insights at both single-cell and subcellular resolutions.

The Xenium Analyzer, our state-of-the-art instrument, swiftly generates data immediately after the run. Whether your tissues are FFPE or fresh frozen (FF), the processing preserves the structural integrity, facilitating additional assays such as H&E, IF, or Visium on the same sample.

Please contact us for an in-depth discussion of your spatial transcriptomics work at the earliest possible planning stages.

For detailed information about “Xenium Sample Preparation Workflow” please click on the button below.

All the information regarding the available gene panels for both mouse and human, as well as custom panels can be found here: https://www.10xgenomics.com/products/xenium-panels

Spatial Transcriptomics is a cutting-edge molecular profiling method that allows scientists to measure all the gene activity in a tissue sample and map where the activity is occurring. Defining the spatial distribution of mRNA molecules allows to uncover cellular heterogeneity in tissues, tumours, immune cells as well as determine the subcellular distribution of transcripts in various conditions. This information provides a unique opportunity to decipher both the cellular and subcellular architecture in both tissues and individual cells.

Collaborating seamlessly with CF-PTA (learn more here), CF-Genomics offers sample processing services for spatial transcriptomics, leveraging the revolutionary 10x Genomics Xenium in situ technology. This process involves the hybridization of several hundred probes, subsequently ligated, amplified, and identified through multiple rounds of probe hybridization and removal. This intricate procedure enables the simultaneous analysis of several hundred transcripts, providing unparalleled insights at both single-cell and subcellular resolutions.

The Xenium Analyzer, our state-of-the-art instrument, swiftly generates data immediately after the run. Whether your tissues are FFPE or fresh frozen (FF), the processing preserves the structural integrity, facilitating additional assays such as H&E, IF, or Visium on the same sample.

Please contact us for an in-depth discussion of your spatial transcriptomics work at the earliest possible planning stages.

For detailed information about “Xenium Sample Preparation Workflow” please click on the button below.

All the information regarding the available gene panels for both mouse and human, as well as custom panels can be found here: https://www.10xgenomics.com/products/xenium-panels

Spatial Transcriptomics Overview

We provide following spatial transcriptomics services:
  • Xenium In Situ for FFPE Tissues
  • Xenium In Situ for Fresh Frozen Tissues

Tissue quality, sectioning and proper gene panel selection are essential for a high-quality output.  We strongly recommend working with CF-PTA for sample collection and/or sectioning the samples. The user has the option to send their own blocks, in this case, a histological QC will be performed by the CF-PTA before the experiment.

The 10x Genomics kits used for a Xenium run are provided to the CF-Genomics by the user. This includes:

  • Xenium Slides & Sample Prep Reagents (PN 1000460)                    
  • Xenium Decoding Reagents (PN 1000461)                                          
  • Xenium Decoding Consumables ( PN 1000487)                                   
  • Gene panels (see below) (PN variable)                                             
  • [optional] Cell segmentation kit (PN 1000662)                                      

Gene panel selection, the user should consider two aspects. First, the genes included in the assay: pre-designed, Add-On (requires Predesigned Panel for Design), Standalone custom panel or Xenium Advanced Upgrades. Second, the number of reactions the user can buy: 2, 4 or 16.

It is possible to ship the reagents directly to CF-Genomics once the service is confirmed. Contact us to ensure space availability.

After the Xenium run is complete, the user has several options: can collect the slides, CF-PTA can perform an H&E or an IF post-run. It is important to be aware that the IF success is not guarantee as it depends on the antibody quality and its ability to perform well after the Xenium run and this is antibody specific.

The following links may also help you for an overview of the Xenium spatial transcriptomics technology and experimental details:

Xenium overview

Panel design

Tissue preparation for Xenium FFPE

Tissue preparation for Xenium FF

Xenium Assay

Xenium Analyzer

 

The Xenium run generates a folder per region analyzed (one slide can have up to 8 regions) in Output Folder. Two output formats that are commonly used:

  • The Analysis summary: this is the interactive immediate output that the Xenium generates during the run. It contains summary metrics and automated secondary analysis results. Any alerts issued by the pipeline are displayed at the top of the page.
  • The experiment.xenium is an experiment manifest file in JSON format that includes experiment metadata and relative file paths to other data files in the output folder needed by Xenium Explorer to visualize results.

For more information about the output data and the output formats, please see the section Understanding Xenium Outputs.

Data transfer: user will get a link, via e-mail, where the data can be downloaded.

 Instruments run by Core Staff only:

  • Xenium Analyzer (10X Genomics)
  • Visium CytAssist (10X Genomics)

Our Contact

AdobeStock_302975834.jpeg

Core Facility Genomics

Ingolstädter Landstraße 1 85764 Neuherberg, Building 34 & 35.37