10x Genomics Xenium for FFPE User Guides
Andrew Houston
Abstract
Xenium allows for in situ transcript detection of selected probe set of RNA targets revealing spatially resolved expression patterns at nearly single-cell resolution.
Steps
Tissue processing and QC
Determine suitable samples of interest by performing a test described in CG000578, sectioning guidelines described in Step 1 pgs. 18-25 and H&E staining in Appendix pgs. 38-45
CG000578_Demonstrated_Protocol_XeniumInSituProtocolsFFPE_TissuePreparationGuide_Rev_C.pdf
Evaluate section and staining quality, only choose samples or regions free of detachment or artifacts
Xenium slide preparation
Utilize CG000578 for section placement on Xenium slides, follow Step 3, pgs. 29-33
After drying slide overnight or up to 4 weeks, proceed with deparaffinization and decrosslinking steps found in CG000580 CG000580_Demonstrated_Protocol_Xenium_FFPE_Deparaffinization_Decrosslinking_RevC.pdf
Immediately following decrosslinking start to prepare probes of interest as outlined in CG000582 CG000582_XeniumInSitu_GeneExpression_UserGuide_RevE.pdf
Initiate probe hybridization overnight, continue with the protocol the next day
Xenium analyzer
Prepare Xenium instrument as outlined in CG000584CG000584_Xenium_Analyzer_UserGuide_RevD.pdf
Load slides and initiate sample scan
