Preview Data: FFPE Human Lung Cancer with Xenium Multimodal Cell Segmentation
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 2.0.0
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Overview
This dataset is a preview of the Xenium multimodal cell segmentation solution using a development version of the assay user guide and analysis software.
How to view data
Interactively explore this dataset with the Xenium Explorer web demo ("Open web demo" above) or download the files to explore further on your desktop. Desktop Xenium Explorer v2.0 is required to view this dataset on your local computer - now available for download here.
See the Getting Started with Xenium Explorer page for general guidance navigating the web demo interface and these instructions to explore the aligned H&E image in the demo.
Biomaterials
FFPE tissue microstrips from multiple tissue samples were embedded within a single FFPE donor block. The selected section represents adult human Lung Adenocarcinoma tissue purchased from BioIVT.
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).
Probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following a development version of the Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide.
Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613). Note: The H&E image may not align perfectly to the morphology image in places where the H&E-stained tissue shrunk, which may be caused by slides drying during the H&E staining workflow.
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 2.0.0.
| Metric | Adenocarcinoma |
|---|---|
| Median transcripts per cell | 46 |
| Cells detected | 162,254 |
| Nuclear transcripts per 100 µm² | 89.9 |
| High quality decoded transcripts detected | 10,605,483 |
| Region area (µm²) | 30,260,670 |
This dataset is licensed under the Creative Commons Attribution license.