Jan 15, 2026
KAPP-Sen TMC: 10x Xenium Prime with Segmentation Kit
- Santhosh Sivajothi1,
- Emily Soja1,
- Allison McNeilly1,
- Grace Frohock1,
- Shruti Bhargava1,
- William F Flynn1,
- Elise T Courtois1
- 1Single Cell Biology Lab, The Jackson Laboratory, USA
- Cellular Senescence Network (SenNet) Method Development Community
- KAPP-Sen TMC
Protocol Citation: Santhosh Sivajothi, Emily Soja, Allison McNeilly, Grace Frohock, Shruti Bhargava, William F Flynn, Elise T Courtois 2026. KAPP-Sen TMC: 10x Xenium Prime with Segmentation Kit . protocols.io https://dx.doi.org/10.17504/protocols.io.n92ld1mr9l5b/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: January 14, 2026
Last Modified: January 15, 2026
Protocol Integer ID: 238659
Keywords: SenNet KAPP-Sen TMC, situ spatial transcriptomic analysis of tissue section, 10x genomics xenium platform, 10x xenium v1 with segmentation kit, integrated 10x genomics workflow, resolution spatial gene expression profiling, 10x genomics workflow, detailed molecular characterization of tissue architecture, spatial gene expression profiling, spatial transcriptomic analysis, 10x xenium v1, tissue architecture, tissue section, segmentation kit, tissue processing, sen tmc, enabling detailed molecular characterization, xenium segmentation kit for accurate cell segmentation, 10x xenium prime with segmentation kit, xenium segmentation kit, broad transcriptomic coverage, 10x xenium prime, 5k standard human gene panel, accurate cell segmentation, gene add
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. The 10x Genomics Xenium platform was employed for high-resolution spatial gene expression profiling, enabling detailed molecular characterization of tissue architecture. The analysis utilized the Xenium Segmentation Kit for accurate cell segmentation, the 5k Standard Human Gene Panel for broad transcriptomic coverage, and an additional 100-gene add-on panel to enhance detection of specific targets of interest.
Troubleshooting
Section preparation
Block handling, QC, and sectioning were performed according to CG000758 Rev E.
After sectioning, slides were placed in a slide drying rack and baked at 42°C for 3 hours, then placed in a desiccator at room temperature overnight.
Xenium In Situ
The assay was performed following Deparaffinization & Crosslinking according to CG000758 Rev E, section 4, immediately followed by probe priming, polishing, hybridization, ligation, and amplification according to CG000760 Rev C, then cell segmentation staining and quenching according to the same protocol.
The Xenium Analyzer was utilized according to CG000584 Rev J.