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--- submission:10x_xenium [2025/02/12 12:02] – skelto01
+++ submission: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======
-X 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.
+X 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):
-[[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=====
-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.
 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 ^
-|Xenium In Situ Gene Expression for 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\\  * Xenium standalone custom gene 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 In Situ Gene Expression v1.0**\\ 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\\  * Xenium standalone custom gene 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)|
 ^Workflow ^Kit Used ^Slide used for submission ^Customization Options ^Post-Xenium Options ^
-|Xenium Prime In Situ Gene Expression for 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)|
-x 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**    ^
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 |Xenium Prime 5K Human Pan Tissue & Pathways|   5001   |
 |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=====
 You'll find information below to help you fill out each part of the Xenium submission form which you can