Xenium Analyzer

Xenium Analyzer

• How can I automate file transfer after a Xenium run completes?
• How are shared network drives mounted on the Xenium Analyzer instrument?
• How do I thaw Xenium Decoding Module B prior to a Xenium Analyzer run?
• What is the purpose of a Xenium Analyzer Readiness Test and how can I perform it?
• Is internet connectivity required for the Xenium Analyzer?
• How do I predict Xenium Analyzer instrument run time?

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General

• Are Xenium slides charged or coated?
• Can different panels be run sequentially on the same tissue section?
• Can different panels be selected on the same Xenium Analyzer run?
• Can different tissue types be run on a single Xenium Slide?
• Can signal be generated from probe hybridization events with genomic DNA?
• Can slides be further processed with H&E staining or another stains after a Xenium Analyzer run?

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Software

• What are the Xenium image scale factors?
• What is the Xenium ‘Negative control probe counts per control per cell’ metric?
• How can I get Xenium probe sequences from the BED file?
• How does Xenium perform cell segmentation?

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?

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Tissue-specific Tips and Tricks

• 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

• How should I store Xenium slides once FFPE tissue sections have been placed?
• What fixation and embedding methods are compatible with Xenium using FFPE tissue inputs?

Tissue Preparation - Fresh Frozen

• How should I store Xenium slides once fresh frozen tissue sections have been placed?

Reagents

• Can I substitute MilliQ 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?
• What alternative TE buffers can be used for Xenium?
• What can I use in place of Probe Dilution Buffer?

Imaging

• Does Xenium Analyzer acquire multiple Z stacks?
• For H&E performed after a Xenium Analyzer run, what imaging requirements are recommended? 
• What kind of microscope does the Xenium Analyzer use?
• What is the composition of the Xenium Analyzer imaging buffer?
• How does the optics system work on the Xenium Analyzer?

Troubleshooting

• What should I do if I cover fiducials on the Xenium slide?
• The adjusted negative control probe rate appears elevated, what does this mean?