10X Xenium in situ tissue samples are processed across both the Histopathology and Genomics cores, with Histopathology sectioning & imaging the slides and the Single Cell Team preparing the slides & running them on the Xenium instrument.

It's very important prior to submission to contact the Single Cell Team & Histology teams.

Initially we would also recommend arranging to discuss your experimental aims with both teams by discussing this at a experimental design meeting (EDM): Request EDM

This will help to ensure that we can jointly advise for your project and coordinate across our respective core teams to get the best options for your submitted tissue & the technology.

We have on-going projects using the Xenium but operate on an equitable use policy such that we can make time for new projects to get access to the technology.

The Xenium process differs depending on whether optional cell segmentation is chosen or Xenium Prime (5K) is the chosen slide & panel. 10x Genomics also offer standalone or add-on custom panels if your genes/ targets of interest are not part of the off-shelf panels. These custom panels are created by 10x and require you to reach out and provide either SC-RNA-seq data, Bulk-RNA-seq or even gene/target names. You can then liaise with us to order this custom set to include in your project. The link to initiate this process is here: https://www.10xgenomics.com/support/software/xenium-panel-designer/latest

The main impact is the time it takes to process samples & slides as well as the subsequent run times and analysis step before data is available. A brief summary of the differences are below but please contact the team if you would like further information.

These panels as well as the target within can be found here:

https://www.10xgenomics.com/support/software/xenium-panel-designer/latest/tutorials/pre-designed-xenium-v1

https://www.10xgenomics.com/support/software/xenium-panel-designer/latest/tutorials/pre-designed-xenium-prime-5k

Xenium add-on and standalone custom panels can be ordered in pack sizes sufficient for 4 or 16 slides.
Please contact the Single Cell Team Single Cell Team to discuss ordering an add-on or custom panel once you have created it with 10x Genomics.

You'll find information below to help you fill out each part of the Xenium submission form which you can download here.

* Pre-designed Probe Panel: Only select an option if you are using a 10x Genomics pre-designed panel as listed above.
* Custom Panel: Only applies if you are using a standalone or add-on custom panel. Input the design unique Panel ID provided by 10x when you order the custom panel.
* Number of Custom Probes: Only applies if you are using a standalone or add-on custom panel. Input the number of genes (plex) in the panel. If using an add-on custom panel, only include the number of genes in the custom panel, not the pre-designed panel.
* Post-Xenium H&E Staining and Post-Xenium IF Staining: This tells us if you would like us to hand your slides back to the histopathology core facility after the Xenium run has finished to perform H&E or IF staining on the same section of tissue. Type ‘Yes’ or ‘No’ in both boxes.
* Sample Source: This tells us if the tissue has been stored as FF, fixed frozen or FFPE.
* HTA: Type ‘Yes’ if your tissue falls under the Human Tissue Act.
* Species: Choose from the drop down menu. If the species you work with is not listed, please choose ‘Other’.
* Billing Information: This is critical for correct invoicing: please follow the popup instructions in the field. If you do not have a SWAG/SWAK code, please contact us to discuss.
* PO number: Only enter a PO number if applicable to your department or organisation. Leave PO number blank if it does not apply! Resist the temptation to put “N/A” or “None”: it will complicate your bills.

* Name: Name of the sample or tissue section being imaged.
* RGT Number: This is provided by the histopathology core (CRUN number) or Tissue Bank (RGT number) when the tissue section has been fixed on the slide. Format of RGT00xxxxxx or CRU00xxxxx. If your sample falls under HTA you have to fill this filed.
* RGT Aliquot Number: Also provided by histopathology – three-digit code after the RGT or CRU number (leave empty if you do not have that information).
* Slide ID: Any additional slide ID provided eg. CRU number or what is written on the slide.
* Number of regions: If you plan to place multiple tissue sections on the same xenium slide, we will treat these as ‘regions’. Please state how many regions are on the same slide.
* DV200: Please provide this if you have done an RNA extraction and Tapestation QC on a tissue section from the same block, to give us an idea of the RNA quality of your tissue sample.
* Species: only complete this if it is different from the species provided in sample set information.
* TMA or Whole Section: Please let us know if you are submitting tissue microarrays or whole sections of tissue on the xenium slide.
* Submission comments: Anything else that needs to be communicated and might be relevant for the experiment.