Jul 17, 2025
JAX-Sen: 10x Xenium V1 with Segmentation Kit
- 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
Protocol Citation: Emily Soja, Shruti Bhargava, Santhosh Sivajothi, William F Flynn, Elise T Courtois 2025. JAX-Sen: 10x Xenium V1 with Segmentation Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvjey2pgk5/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: July 15, 2025
Last Modified: July 17, 2025
Protocol Integer ID: 222587
Keywords: 10x genomics xenium platform, 10x xenium v1 with segmentation kit, situ spatial transcriptomic analysis of tissue section, integrated 10x genomics workflow, 10x genomics workflow, resolution spatial gene expression profiling, 10x xenium v1, spatial gene expression profiling, detailed molecular characterization of tissue architecture, spatial transcriptomic analysis, tissue architecture, xenium, tissue section, segmentation kit, tissue processing, enabling detailed molecular characterization
Funders Acknowledgements:
The Jackson Laboratory Senescence Tissue Mapping Center (JAX-Sen TMC)
Grant ID: U54AG079753
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.
Guidelines
This protocol needs prior approval by the users' Institutional Animal Care and Use Committee (IACUC) or equivalent ethics committee.
Troubleshooting
Safety warnings
This protocol needs prior approval by the users' Institutional Animal Care and Use Committee (IACUC) or equivalent ethics committee
Section Preparation
Block QC and sectioning according to CG000578 Rev E.
Post sectioning, all slides were dried overnight at 37C then put in the desiccator.
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.
The segmentation kit staining is performed according to CG000749 Rev B.
Xenium Analyzer is used according to CG000584 Rev H.
10X Genomics, Xenium Mouse Multi-Tissue Atlassing Panel , PN: 1000627 was used. This panel had 379 genes while the custom add-on panel had 100 genes.