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FFPE Human Breast using the Entire Sample Area

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.0.2

Click "Open web demo" to view our FFPE human breast Xenium Explorer demo in your browser.Learn about the demo sample biology here.
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Demonstration of the Xenium platform's large imaging sample area, which enables high resolution and high throughput gene expression profiling. Replicate results demonstrate the high reproducibility of data generated by the platform.

The data were generated with the pre-designed Xenium Human Breast Gene Expression Panel (v1).

5µm sections from a formalin-fixed paraffin-embedded (FFPE) human breast resected tumor mass sample:

  • Infiltrating Ductal Carcinoma (from Avaden Biosciences)

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 Replicate tabs. 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 or image alignment file in Xenium Explorer.

Key metrics

MetricReplicate 1Replicate 2
Median transcripts per cell10097
Cells detected892,966885,523
Decoded transcripts per 100 µm²58.856.6
Total transcripts detected105,584,672100,634,191
Scanned tissue area (cm²)2.282.21

This dataset is licensed under the Creative Commons Attribution license.