FFPE Human Breast Cancer with 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 3.0.0
Learn about Xenium analysis
Overview
Xenium Prime 5K In Situ Gene Expression with Cell Segmentation data for human breast cancer (FFPE) using the Xenium Prime 5K Human Pan Tissue and Pathways Panel plus 100 Custom Genes.
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-preserved tissue blocks were purchased from Discovery Life Sciences (Breast Cancer: II-A (T1c N1 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).
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 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.
The 100 gene custom panel was selected based on differentially expressed genes from serial section matched Flex data from four tissue types: ovarian, cervical, breast, and uterine cancers. In addition, HPV16/18 probes were included for cervical cancer (based on information from the biobank where the FFPE tissue blocks were sourced).
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 | Breast cancer |
|---|---|
| Median transcripts per cell | 51 |
| Cells detected | 699,110 |
| Nuclear transcripts per 100 µm² | 196.3 |
| High quality decoded transcripts detected | 80,158,637 |
| Region area (µm²) | 155,159,780.8 |
This dataset is licensed under the Creative Commons Attribution license.