Xenium FFPE Human Breast with Custom Add-on Panel

Demonstration of gene expression profiling for a formalin-fixed paraffin-embedded (FFPE) human breast sample on the Xenium platform. This dataset was re-run with Xenium Onboard Analysis v1.3 software.

The data were generated with the pre-designed panel plus an add-on panel of 100 custom genes. The same experiment was also run with the pre-designed Xenium Human Breast Gene Expression (v1) panel.

5µm section from a resected tumor mass tissue:

• Infiltrating ductal carcinoma (IDC), Ductal carcinoma in situ (from BiolVT)

The tissue was 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). The registered H&E image file provided below is suitable for annotating regions. It may or may not be suitable for more refined exact sub-cellular resolution correspondence due to minute differences in the optics of the microscopy systems. Learn more in the H&E to Xenium DAPI Image Registration with Fiji Analysis Guide.

How to view data

Panel and gene groups files are displayed in the Inputs/Slide tab and the sample output files are in the Tissue tab. The panel.csv file contains a list of the custom genes added to the pre-designed panel. Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle file. Load the Gene Groups CSV to create gene groups based on cell type markers. Follow these instructions to view the aligned post-Xenium H&E image in Xenium Explorer.

Key metrics

• Median transcripts per cell - 119
• Cells detected - 576,963
• Decoded transcripts per 100 µm² - 105.5
• Total transcripts detected - 77,995,296
• Scanned tissue area (cm²) - 0.96

This dataset is licensed under the Creative Commons Attribution license.