Mar 01, 2024

Public workspace10x Genomics Xenium for FFPE User Guides

DOI
https://dx.doi.org/10.17504/protocols.io.81wgbxjonlpk/v1
  • Andrew Houston1
  • 1Department of Medicine, Washington University in St. Louis
Andrew Houston
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DOI: https://dx.doi.org/10.17504/protocols.io.81wgbxjonlpk/v1
Protocol Citation: Andrew Houston 2024. 10x Genomics Xenium for FFPE User Guides. protocols.io https://dx.doi.org/10.17504/protocols.io.81wgbxjonlpk/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 01, 2024
Last Modified: March 01, 2024
Protocol Integer ID: 96033
Keywords: probe set of rna target, ffpe user guides xenium, situ transcript detection, rna target, rna, genomic, ffpe, cell resolution, 10x
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.
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
Download CG000578_Demonstrated_Protocol_XeniumInSituProtocolsFFPE_TissuePreparationGuide_Rev_C.pdfCG000578_Demonstrated_Protocol_XeniumInSituProtocolsFFPE_TissuePreparationGuide_Rev_C.pdf8.3MB

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 Download CG000580_Demonstrated_Protocol_Xenium_FFPE_Deparaffinization_Decrosslinking_RevC.pdfCG000580_Demonstrated_Protocol_Xenium_FFPE_Deparaffinization_Decrosslinking_RevC.pdf7MB

Immediately following decrosslinking start to prepare probes of interest as outlined in CG000582 Download CG000582_XeniumInSitu_GeneExpression_UserGuide_RevE.pdfCG000582_XeniumInSitu_GeneExpression_UserGuide_RevE.pdf7.8MB
Initiate probe hybridization overnight, continue with the protocol the next day

Xenium analyzer
Prepare Xenium instrument as outlined in CG000584Download CG000584_Xenium_Analyzer_UserGuide_RevD.pdfCG000584_Xenium_Analyzer_UserGuide_RevD.pdf13.3MB

Load slides and initiate sample scan