Feb 27, 2026
KAPP-Sen TMC: 10x Genomics Visium HD Spatial Gene Expression on FFPE tissues
- Emily C. Soja1,
- Paul Gabriel1,
- Jessica Grassmann1,
- William F. Flynn1,
- Elise T. Courtois1
- 1Single Cell Biology Lab, The Jackson Laboratory, USA
- Cellular Senescence Network (SenNet) Method Development Community
Protocol Citation: Emily C. Soja, Paul Gabriel, Jessica Grassmann, William F. Flynn, Elise T. Courtois 2026. KAPP-Sen TMC: 10x Genomics Visium HD Spatial Gene Expression on FFPE tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgq1qzyvk5/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: February 26, 2026
Last Modified: February 27, 2026
Protocol Integer ID: 244118
Keywords: KAPP-Sen TMC, spatial transcriptomic profiling from tissue section, 10x genomics visium hd spatial gene expression, visium hd spatial gene expression the assay, 10x cytassist instrument for spatial gene expression profiling, spatial gene expression profiling, visium hd spatial gene expression, spatial transcriptomic profiling, spatial mapping reconstruct transcriptomic pattern, transcriptomic pattern, single cell biology lab at the jackson laboratory, ffpe tissue, detailed analysis of tissue organization, single cell biology lab, visium hd assay, genomic, tissue section, tissue organization, genomic medicine
Funders Acknowledgements:
National Institute on Aging (NIA) KAPP-Sen Tissue Mapping Collaborative
Grant ID: U54 AG075941
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Abstract
The Visium HD assay enables high‑resolution spatial transcriptomic profiling from tissue sections on a dense array of spatial barcodes. Tissue is sectioned, H&E stained, scanned, and processed on the 10x CytAssist instrument for spatial gene expression profiling. Subsequent sequencing and spatial mapping reconstruct transcriptomic patterns at near‑cellular (2 µm) resolution, supporting detailed analysis of tissue organization and cell states.
Tissue sections are processed with Visium HD Spatial Gene Expression the assay performed by the Single Cell Biology Lab at The Jackson Laboratory for Genomic Medicine.
Troubleshooting
Procedure
Tissue sectioning, Deparaffinization, H&E, Decrosslinking according to:
Visium HD FFPE Tissue Preparation Handbook CG000684 Rev A.
Library Preparation according to:
Visium HD Spatial Gene Expression Reagent Kits User Guide CG000685 Rev A.
Library Sequencing:
Libraries are pooled for sequencing on an Illumina NovaSeq sequencer instrument. Sequencing these libraries produces a standard Illumina BCL data output folder.