Example Xenium In Situ Gene Expression datasets are available for download on the 10x datasets webpage. They cover a range of tissue types and states, pre-designed and custom gene panel designs, and Xenium Onboard Analysis (XOA) software versions. Several include post-Xenium H&E and/or IF images and image alignment files that can be opened directly in Xenium Explorer.
Here, we provide datasets that have been trimmed down to a few FOVs from larger datasets. These datasets are intended to demonstrate output file format changes introduced by new versions of XOA pipeline software on the Xenium Analyzer (XA) instrument. They can be used to test code dependencies on these output formats. Since these datasets are trimmed, they are not meant to be used to draw biological conclusions. For each dataset, .zip file size and md5sum information are provided with the download link.
These datasets are licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.
These datasets were each artificially subset to three 640 pixel square patches across two FOVs. Metrics and metadata are only for demonstrating XOA v4.0 output file formats.
| Gene panel | Assay user guide | Cell segmentation algorithm | Download information |
|---|---|---|---|
| Xenium Human Multi-Tissue and Cancer Panel + Custom Addon | CG000819 Protein: Xenium Immune Checkpoint Subpanel | Multimodal | 20 MB, 50c04dea5e751e1c7508ff24528242e8 Download here |
| Xenium Human Immuno-Oncology Profiling Panel + Custom Addon | CG000749 | Multimodal | 29 MB, c0af4c72bed2c7fb4eb6d9f1fdf3b2e1 Download here |
| Xenium Human Immuno-Oncology Profiling Panel + Custom Addon | CG000582 | Nuclear expansion (5 µm) | 27 MB, a1de61c57b468450ba1fbcdcc1d7c811 Download here |
Download with command line:
# Human kidney, Xenium In Situ Gene and Protein Expression with Cell Segmentation Staining
curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip
# Human ovary, Xenium In Situ Gene Expression with Cell Segmentation Staining
curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip
# Human ovary, Xenium In Situ Gene Expression, nuclear expansion
curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip
These datasets were each artificially subset to three 160 pixel square patches across two FOVs. Metrics and metadata are only for demonstrating XOA v3.0 output file formats.
| Panel | Assay User Guide | Cell segmentation algorithm | Download information |
|---|---|---|---|
| Xenium Prime 5K Mouse Pan Tissue & Pathways Panel | CG000760 | Multimodal | 11.9 MB, be9d917eaac2ade708c111132f0f379d Download here |
| Xenium Prime 5K Mouse Pan Tissue & Pathways Panel | CG000760 | Nuclear expansion (5 µm) | 12 MB, 0a7469a005576f2932e4f804dd9bc563 Download here |
Download with command line:
# Mouse ileum, multimodal cell segmentation
curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
# Mouse ileum, nuclear expansion
curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip
These datasets were trimmed down to two FOVs:
| Panel | Assay User Guide | Cell segmentation algorithm | Download information |
|---|---|---|---|
| Xenium Human Breast Gene Expression | CG000749 | Multimodal | 379 MB, 4632914eca973a1d532231ea646e10cc Download here |
| Xenium Human Lung Gene Expression | CG000582 | Nuclear expansion (5 µm) | 278 MB, bf9c5e6762681b81eab0a19d3d590381 Download here |
Download with command line:
# Xenium Human Breast Gene Expression
curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
# Xenium Human Lung Gene Expression
curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip