FFPE Human Breast with Custom Add-on Panel

Demonstration of gene expression profiling for formalin-fixed paraffin-embedded (FFPE) human breast samples on the Xenium platform.

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 sections from two resected tumor mass tissues:

• Infiltrating ductal carcinoma, Ductal carcinoma in situ (from BiolVT)
• Invasive lobular carcinoma (from Avaden Biosciences)

The 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).

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

Shared files are displayed in the Inputs/Slide tab and per-sample output files are in the Tissue tabs. 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 post-Xenium H&E image in Xenium Explorer.

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