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Human Skin Data with Xenium Human Multi-Tissue and Cancer Panel

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.9.0

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Xenium In Situ Gene Expression data for adult human skin sections using the Xenium Human Multi-Tissue and Cancer Panel.

How to view data

Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle (or Xenium Explorer subset) file. The subset bundle contains the experiment.xenium, morphology_mip.ome.tif, analysis_summary.html,,,, and files. See the Getting Started with Xenium Explorer page for more details. Follow these instructions to view the post-Xenium H&E image or image alignment file in Xenium Explorer.


FFPE-preserved tissues were purchased from Avaden Biosciences (non-diseased skin).

Tissue preparation

Tissues were prepared following the Demonstrated Protocols Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578) and Xenium In Situ for FFPE Tissues – Deparaffinization & Decrosslinking (CG000580). Additional guidance for sectioning skin samples is provided here.

Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).

Gene panels

The Xenium Human Multi-Tissue and Cancer Panel (377 genes) was pre-designed by 10x Genomics. The panel design was informed using single cell RNA sequencing data curated and reprocessed for standardization by the Human Protein Atlas. Genes were chosen to accurately type cells, and identify select immune, proliferation, and tumor markers, in human breast, lung, skin, liver, colon, kidney, lung cancer, and heart.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide (CG000584). The on-instrument analysis was run with Xenium Onboard Analysis version 1.9.0. The analysis summary for both samples shows the "Low decoded transcripts per 100 µm2" warning. This is expected because the epidermis contains very high transcript counts for genes on the panel, but the other cell types in skin have lower counts by comparison. In these two samples, the epidermis is only a fraction of the total surface area of the samples, thus contributing to an overall low number of decoded transcripts per 100 µm2.

MetricSample 1Sample 2
Median transcripts per cell2517
Cells detected68,47690,106
Decoded transcripts per 100 µm²9.88.7
Total high quality decoded transcripts2,113,7211,797,665
Region area (µm²)72,922,73643,243,357

This dataset is licensed under the Creative Commons Attribution license.