Human Liver 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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Overview
Xenium In Situ Gene Expression data for adult human liver 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, 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.
Biomaterials
FFPE-preserved tissues were purchased from Avaden Biosciences (non-diseased liver, liver cancer).
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).
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. The liver cancer dataset was generated with the Xenium Human Multi-Tissue and Cancer Panel plus an add-on panel of 97 custom genes to simulate the utilization of a typical customer add-on panel.
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.
| Metric | Non-diseased | Liver cancer |
|---|---|---|
| Median transcripts per cell | 80 | 114 |
| Cells detected | 239,271 | 162,628 |
| Decoded transcripts per 100 µm² | 38.0 | 85.0 |
| Total high quality decoded transcripts | 21,208,519 | 21,223,431 |
| Region area (µm²) | 70,642,593 | 33,656,162 |
This dataset is licensed under the Creative Commons Attribution license.