Questions & Answers
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SupportIn Situ Gene Expression
Subcellular profiling of targeted features from fresh frozen or FFPE tissues.
Xenium Analyzer
Xenium Analyzer
- Can I monitor the progress of my Xenium Analyzer run?
- What is the approximate weight of Xenium Decoding Modules?
- How does slide storage or rerunning slides on the Xenium Analyzer impact data?
- How do I know if Decoding Module plates have been loaded correctly?
- How do I transfer data via USB on Xenium Analyzer instruments on SW version 1.8 and up?
- How can I automate file transfer after a Xenium run completes?
General
- Can different gene expression panels be selected on the same Xenium Analyzer run?
- Can different panels be run sequentially on the same tissue section?
- Can I ship slides after the Xenium assay workflow?
- How can Xenium slides be stored prior to a Xenium Analyzer run?
- How much does the post Xenium-Analyzer run H&E differ from H&E on totally unprocessed tissue?
- How should unused Xenium slides be stored?
Software
- How do you integrate multiple samples for Xenium analysis?
- How can I convert coordinates between H&E image and Xenium data?
- Why is Xenium Explorer telling me it “Cannot open required files”?
- XOA v3.2 datasets do not require batch correction to be analyzed with previous XOA v3 datasets
- Xenium Multimodal Cell Segmentation on muscle
- Import annotations into Xenium Explorer
Software: Panel Designer
- Xenium advanced custom target probe design feasibility
- Why can’t we design Xenium probes or enough probes for certain genes?
- Can gene expression of microbes be profiled spatially?
- How to interpret common Upload Reference Dataset error messages in Xenium Panel Designer
- How do I facilitate a fast advanced custom panel design turn around?
- Gene causes optical crowding in Xenium panel design
Tissue and Sample Preparation
- Are fixed tissues embedded in OCT compatible with Xenium?
- Are alternative autofluorescence quenching protocols compatible with Xenium?
- How can I avoid mRNA degradation during sample preparation and slide processing for Xenium In Situ?
- How do I ship Xenium slides with tissue sections?
- How do I study large tissue sections using Xenium?
- How can I more easily visualize the fiducial frame on Xenium slides?
Tissue-specific Tips and Tricks
- What should I consider when processing Human Brain on Xenium?
- Can Xenium In Situ Gene Expression data be generated from PBMCs?
- Can cells be adhered to Xenium slides to obtain gene expression data?
- Do you have recommendations for sectioning skin for Xenium?
- Do you have recommendations for organoids for Xenium?
- Do you have recommendations for sectioning TMAs for Xenium?
Tissue Preparation - FFPE
- Do you have recommendations for FFPE tissue fixation for Xenium?
- Do you have tips and tricks for pre-fixation tissue handling for Xenium?
- How does delayed fixation impact Xenium performance?
- How should I store Xenium slides once FFPE tissue sections have been placed?
- How to generate tissue arrays for Xenium?
Tissue Preparation - Fresh Frozen
Reagents
- Can I substitute Milli-Q water for nuclease-free water in the Xenium workflow?
- Can I use 100% Tween 20 diluted to 10% Tween 20 for Xenium?
- Can I use alternative third-party reagents for Xenium?
- Can I use Neo-Clear as an alternative to xylene for Deparaffinization with Xenium In Situ Gene Expression?
- Does the change in Xenium v1 custom probe panel resuspension buffer or volume impact Xenium performance?
- How many freeze-thaw cycles are Xenium reagents stable for?
Imaging
Multimodal Cell Segmentation
- Are we providing clonotype information of the antibodies used in the Multi-tissue Cell Segmentation Stain Mix?
- Can I use a Cassette Lid instead of PCR film during Cell Segmentation Staining?
- Does the cell segmentation add-on kit work with organisms other than human and mouse?
- Can additional antibodies or alternative stains be spiked into the multi-tissue cocktail?
- Will the fluorescent signal from the segmentation stain interfere with the detection of genes?