Jun 03, 2025

Public workspaceKAPP-Sen TMC: 10x Xenium V1 with Segmentation Kit 

DOI
dx.doi.org/10.17504/protocols.io.x54v9o68zv3e/v1
  • Emily Soja1,
  • Shruti Bhargava1,
  • Santhosh Sivajothi1,
  • William F Flynn1,
  • Elise T Courtois1
  • 1Single Cell Biology Lab, The Jackson Laboratory, USA
  • Cellular Senescence Network (SenNet) Method Development Community
  • KAPP-Sen TMC
Sergii Domanskyi
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DOI: dx.doi.org/10.17504/protocols.io.x54v9o68zv3e/v1
Protocol Citation: Emily Soja, Shruti Bhargava, Santhosh Sivajothi, William F Flynn, Elise T Courtois 2025. KAPP-Sen TMC: 10x Xenium V1 with Segmentation Kit . protocols.io https://dx.doi.org/10.17504/protocols.io.x54v9o68zv3e/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: June 03, 2025
Last Modified: June 03, 2025
Protocol Integer ID: 219494
Keywords: SenNet KAPP-Sen TMC
Funders Acknowledgements:
National Institute on Aging (NIA) KAPP-Sen Tissue Mapping Collaborative
Grant ID: U54 AG075941
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Abstract
This protocol describes the preparation, staining, and in situ spatial transcriptomic analysis of tissue sections using an integrated 10x Genomics workflow. Standardized procedures were followed for tissue processing, slide preparation, and staining to ensure consistency and quality. Modifications were applied where appropriate to optimize sample integrity. The 10x Genomics Xenium platform was employed for high-resolution spatial gene expression profiling, enabling detailed molecular characterization of tissue architecture.
Section preparation
Section preparation
Block QC and sectioning according to CG000578 Rev E.
Post sectioning, all slides are baked at 42°C for 3 hours.
Xenium In Situ
Xenium In Situ
Deparaffinization and decrosslinking is done according to CG000580 Rev E. Deparaffinization temperature and time is according to this 10x protocol, 60°C for 2 hours.

Note
We perform decrosslinking according to this KB article, which recommends using 37°C for 30 minutes instead of the protocol’s recommended 80°C for 30min.


Critical
The segmentation kit staining is performed according to CG000749 Rev B.
Xenium Analyzer is used according to CG000584 Rev H.