Human Skin Preview Data (Xenium Human Skin Gene Expression Panel with Custom Add-On)
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.7.0
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Overview
Preview of Xenium In Situ Gene Expression data for adult human skin sections, using a development version of the Xenium Human Skin Gene Expression Panel.
Biomaterials
FFPE-preserved tissues were purchased from Avaden Biosciences (Melanoma).
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 Skin Gene Expression Panel (282 genes) was pre-designed by 10x Genomics. Genes were chosen to prioritize identification of keratinocytes, melanocytes, fibroblasts, Langerhans cells, vascular endothelial, immune cells and other cell types in human normal skin, melanoma, basal cell carcinoma, and squamous cell carcinoma. The pre-designed panel was supplemented with an additional 100 genes, including chemokine genes, cytokine genes, and markers for immune cell subtypes.
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 1.7.0. The data were reanalyzed with Xenium Ranger to reduce false positive cells in the dermis using the xeniumranger resegment pipeline and a --dapi-filter of 400.
| Metric | Melanoma, pre-designed panel + add-on |
|---|---|
| Cells detected | 87,499 |
| Decoded transcripts per 100 µm² | 157.0 |
| Median transcripts per cell | 122 |
| Total high quality decoded transcripts | 13,706,786 |
| Region area (µm²) | 12,753,959 |
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, cells.zarr.zip, cell_feature_matrix.zarr.zip, transcripts.zarr.zip, and analysis.zarr.zip 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.
This dataset is licensed under the Creative Commons Attribution license.