CRUK-CI Genomics Help

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submission:10x_xenium [2025/02/12 11:48] – 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.
 +{{:xenium_workflow2.png?920|}}
 +{{:xenium_workflow_without_segmentation2.png?920|}}
  
  
-{{:submission:xenium_workflow2.jpg?920|}} 
  
  
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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 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 ^ ^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)|
- +
-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 
 [[https://genomicsequencing.cruk.cam.ac.uk/sequencing/forms/DownloadForm.action |download here.]] [[https://genomicsequencing.cruk.cam.ac.uk/sequencing/forms/DownloadForm.action |download here.]]
  
-* **Pre-designed Probe Panel:**\\  Only select an option if you are using a 10x Genomics pre-designed panel as listed above.\\  +* **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.\\  
-* **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 
-* **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.\\  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.\\  
-* **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’.\\ 
-* **HTA:** \\ Type ‘Yes’ if your tissue falls under the Human Tissue Act.\\ +* **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, 
-  +
-* **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.\\ 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 
-* **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.\\ temptation to put "N/A" or "None": it will complicate your bills.\\
  
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 * **Name:** Name of the sample or tissue section being imaged.\\   * **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 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). \\  * **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.\\   * **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.\\  * **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. \\  * **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.\\  * **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.\\  * **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.\\  * **Submission comments:** Anything else that needs to be communicated and might be relevant for the experiment.\\