CRUK-CI Genomics Help

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submission:10x_xenium [2025/02/12 15:46] – skelto01submission:10x_xenium [2025/02/13 18:16] (current) – [Workflow: kits, panels & post xenium options] Bioinformatics service admin
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 ====== Genomics Xenium In Situ Submission====== ====== Genomics Xenium In Situ Submission======
  
-10X Xenium in situ tissue samples are processed across both the Histopathology and Genomics cores,  with histo sectioning & preparing slides & the core genomics single cell team processing & running them on the Xenium instrument. +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 [[singlecell@cruk.cam.ac.uk|single cell team]] & [[histopathology@cruk.cam.ac.uk|histology]] teams.\\ +**It's very important prior to submission** to contact the [[singlecell@cruk.cam.ac.uk|Single Cell Team]] & [[histopathology@cruk.cam.ac.uk|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): Initially we would also recommend arranging to discuss your experimental aims with both teams by discussing this at a experimental design meeting (EDM):
-[[experimentaldesign@cruk.cam.ac.uk|request EDM]]\\ +[[experimentaldesign@cruk.cam.ac.uk|Request EDM]]\\ 
  
-This will help to ensure that we can plan & coordinate across our respective core teams to get the best options for your submitted tissue & the technology.+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.
 =====Overview of the 10x Xenium Process===== =====Overview of the 10x Xenium Process=====
-The Xenium process differs depending on whether optional cell segmentation is chosen or Xenium Prime (5K) is the chosen slide & panel. +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. 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. A brief summary of the differences are below but please contact the team if you would like further information.
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 ^Workflow ^Kit Used ^Slide used for submission ^Customization Options ^Post-Xenium Options ^ ^Workflow ^Kit Used ^Slide used for submission ^Customization Options ^Post-Xenium Options ^
 |**Xenium Prime (5K)**\\ Formalin Fixed/Paraffin embedded\\  Formalin Fixed(FFPE) fresh frozen (FF) or fixed frozen (FxF) tissue|* Xenium slides & sample prep reagents\\ * Xenium decoding consumables\\  * Xenium pre-designed gene expression panel\\   * Xenium add on custom panel\\ * Optional cell segmentation |Xenium slide with pre-printed xenium slide ID & 10.45 x22.45mm fiducial frame| *Xenium pre-designed panels (see below)\\  * Add-on custom panels (up to 100 genes)\\  * Standalone custom gene panels (up to 480 genes)\\ | * Haemotoxylin and Eosin (H&E) Staining\\ * 10X Visium\\ *Immunofluorescence (IF)| |**Xenium Prime (5K)**\\ Formalin Fixed/Paraffin embedded\\  Formalin Fixed(FFPE) fresh frozen (FF) or fixed frozen (FxF) tissue|* Xenium slides & sample prep reagents\\ * Xenium decoding consumables\\  * Xenium pre-designed gene expression panel\\   * Xenium add on custom panel\\ * Optional cell segmentation |Xenium slide with pre-printed xenium slide ID & 10.45 x22.45mm fiducial frame| *Xenium pre-designed panels (see below)\\  * Add-on custom panels (up to 100 genes)\\  * Standalone custom gene panels (up to 480 genes)\\ | * Haemotoxylin and Eosin (H&E) Staining\\ * 10X Visium\\ *Immunofluorescence (IF)|
- 
-10x Genomics offer multiple pre-designed panels (in packs sizes sufficient for 2 slides) detailed below:\\ [[https://www.10xgenomics.com/products/xenium-panels/| xenium panels]]\\   
- 
-Xenium add-on custom panels and standalone custom panels can be ordered in pack sizes suffcient for 4 or 16 slides.\\  
-Please contact the Genomics single cell team [[singlecell@cruk.cam.ac.uk|single cell team]] to discuss ordering a add-on or custom panel.  
  
 ^**Pre-designed panel** ^   **Genes targeted**    ^ ^**Pre-designed panel** ^   **Genes targeted**    ^
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 |Xenium Prime 5K Human Pan Tissue & Pathways|   5001   | |Xenium Prime 5K Human Pan Tissue & Pathways|   5001   |
 |Xenium Prime 5K Mouse Pan Tissue & Pathways|   5006   | |Xenium Prime 5K Mouse Pan Tissue & Pathways|   5006   |
 +
 +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 [[singlecell@cruk.cam.ac.uk|Single Cell Team]] to discuss ordering an add-on or custom panel once you have created it with 10x Genomics. 
 =====How to Complete the 10x Xenium Submission Form=====  =====How to Complete the 10x Xenium Submission Form===== 
 You'll find information below to help you fill out each part of the Xenium submission form which you can  You'll find information below to help you fill out each part of the Xenium submission form which you can