Post-Xenium Technical Note: Xenium v1 and Xenium Prime 5K for FFPE Human Lung Cancer
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 3.0.0
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Overview
These datasets are provided as part of the Post-Xenium In Situ Applications: Immunofluorescence, H&E, Visium v2, and Visium HD Technical Note (CG000709, Rev C).
- Experiment 1: Xenium In Situ Gene Expression (Xenium v1) data for adult human lung adenocarcinoma tissue (FFPE) using the Xenium Human Lung Gene Expression Panel with nuclear expansion.
- Experiment 2: Xenium Prime 5K In Situ Gene Expression with Cell Segmentation data for human lung adenocarcinoma tissue (FFPE) using the Xenium Prime 5K Human Pan Tissue and Pathways Panel.
The corresponding Visium HD Spatial Gene Expression datasets that were performed after these Xenium experiments are available here.
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, gene_panel.json, morphology_focus/ directory of multi-file OME-TIFF files, 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
For both experiments, FFPE-preserved tissue was purchased from Avaden Biosciences (Lung Cancer, Invasive Acinar Adenocarcinoma, IB, T2a N0 MX).
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).
- For experiment 1, probe hybridization, washing, ligation, and amplification were performed following the Xenium In Situ Gene Expression User Guide (CG000582).
- For experiment 2, probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following the Xenium Prime In Situ Gene Expression with optional Cell Segmentation Staining User Guide (CG000760).
Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).
Gene panels
The Xenium Human Lung Gene Expression Panel was pre-designed by 10x Genomics to identify cells in healthy, cancer, and fibrotic lung, including epithelial, stromal, endothelial, secretory, immune, and tumor cells.
The Xenium Prime 5K Human Pan Tissue and Pathways Panel was designed to enable comprehensive cell type and cell state identification using publicly available single cell RNA sequencing data. The panel also covers canonical signaling pathways, as well as genes relevant to developmental biology, immuno-oncology, and genes that are well known in biomedical literature.
Xenium Analyzer
The instrument run was performed following the Xenium Analyzer User Guide CG000584. The on-instrument analysis was run with Xenium Onboard Analysis v3.0.0.
| Metric | Experiment 1, Xenium v1 | Experiment 2, Xenium Prime 5K |
|---|---|---|
| Median transcripts per cell | 58 | 242 |
| Cells detected | 278,659 | 278,328 |
| Nuclear transcripts per 100 µm² | 162.2 | 674.5 |
| High quality decoded transcripts detected | 30,871,547 | 149,372,743 |
| Region area (µm²) | 72,022,935.6 | 71,085,050.3 |
This dataset is licensed under the Creative Commons Attribution license.