FFPE Human Pancreas with Xenium Multimodal Cell Segmentation
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 2.0.0
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Overview
Xenium In Situ Gene Expression with Cell Segmentation Staining data for adult human pancreatic cancer tissue 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, 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
FFPE tissue microstrips from multiple tissue samples were embedded within a single FFPE donor block. The selected section represents adult human pancreatic cancer (Stage III Adenocarcinoma) tissue purchased from AcePix Biosciences.
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 the Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749).
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 2.0.0.
| Metric | Pancreas |
|---|---|
| Median transcripts per cell | 31 |
| Cells detected | 140,702 |
| Nuclear transcripts per 100 µm² | 66.4 |
| High quality decoded transcripts detected | 7,170,423 |
| Region area (µm²) | 20,121,068 |
This dataset is licensed under the Creative Commons Attribution license.