Xenium In Situ Datasets

Explore Human Breast Tumors

Use Xenium Explorer Demo, a preview of the upcoming desktop app, to explore a Xenium In Situ dataset from a 0.4cm² tissue area of a human breast cancer sample using a 280-gene Xenium Human Breast Gene Expression Panel with 33 additional custom genes.

Open in Xenium Explorer Demo

This dataset demo is currently not supported on mobile and tablet devices. Please use a computer to explore the dataset.

View or download outputs

human breast tumors
This is a preview of Xenium In Situ data.
This dataset may not be representative of Xenium In Situ expected in late 2022.

Key Metrics

  • Species and tissue
    Human breast
  • Preservation method
    FFPE
  • Off-the-shelf panel used
    Xenium Human Breast Gene Expression Panel (280 genes)
  • Number of custom genes
    33
  • Tissue area
    0.4 cm²
  • Number of cells detected*
    167,782
  • Total transcripts detected*
    34,764,833
  • Median transcripts per cell*
    169
*Metrics may differ slightly from preprint because this dataset was processed using a newer version of the analysis pipeline

Explore cell type heterogeneity with Xenium and verify with H&E staining on the same section.

Different tissue macrostructures are revealed by the spatial organization of cell types and gene features, capturing vast cellular and molecular heterogeneity within tumor regions

Xenium identifies major cell types in the human breast. As shown in two examples, spatial information is necessary to study tumor subtype heterogeneity and the microenvironment surrounding tumor epithelial cells. Interpretation and validation of rich transcript information is assisted by H&E staining acquired post-Xenium.

Cells colored by expression profiles in tSNE space and mapped back to original tissue space
H&E image
Cells colored by expression profiles in t-SNE space and mapped back to original tissue space (top). H&E image of the same section. Scale bar 1 mm (bottom).
Atypical ductal hyperplasia
Atypical ductal hyperplasia
Atypical ductal hyperplasia. Myoepithelial cells (green) are present in healthy breast lining the basal cell layer of epithelium. In hyperplasia, some cells exhibit expression profiles more similar to cells typically found in ductal carcinoma in situ (DCIS).
DCIS (left) in proximity to benign duct ectasia (right)
DCIS (left) in proximity to benign duct ectasia (right)
DCIS (green arrow) in proximity to benign duct ectasia (orange arrow). In duct ectasia, macrophages are detected within the thickened duct wall, surrounded by inflammatory cells. Scale bar 200 μm.

DAPI-based cell segmentation

Xenium uses an in-house trained model to segment nuclei from the DAPI image. Nuclei of irregular shapes are segmented well using Xenium analysis software. Transcripts are assigned based on expansion from nuclei.

DAPI image
DAPI image. Scale bar: 50 μm
DAPI image with nuclear outlines
DAPI image with nuclear outlines. Scale bar: 50 μm
DAPI image with nuclear (green) and cellular (yellow) outline
DAPI image with nuclear (green) and cellular (yellow) outlines. Scale bar: 50 μm

Xenium output can be analyzed in commonly used single cell data analysis software to annotate clusters and/or identify differentially expressed genes.

Top 10 differentially expressed genes in example cell types
Top 10 differentially expressed genes in example cell types

Find triple-positive rare cells

In what is classified as ERBB2(HER2)-positive, ESR1(ER)-positive and PGR(PR)-negative breast tumor, Xenium finds rare triple-positive cells that express all three hormonal receptors.

Transcript view of ERBB2, ESR1, PGR and the rest of gene
Expression level of three genes visualized in tSNE
Transcript view of ERBB2, ESR1, PGR, and other genes. Triple-positive region shown in yellow. Scale bar 1 mm (top). Expression level of three genes visualized in t-SNE. The small population of triple-positive cells are highlighted in white box (bottom).
Triple-positive (ESR1+/PGR+/ERBB2+) DCIS
Double positive (ESR1+/ERBB2+) DCIS
Transcript count and density within the ROI manually drawn using the freehand selection tool in Xenium Explorer. (Top) Triple-positive (ESR1+/PGR+/ERBB2+) DCIS and (bottom) double positive (ESR1+/ERBB2+) DCIS