Fresh Frozen Mouse Colon with Xenium Multimodal Cell Segmentation
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 2.0.0
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Overview
Xenium In Situ Gene Expression with Cell Segmentation Staining data for mouse colon tissue using the Xenium Mouse Tissue Atlassing Panel.
How to view data
Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle (or Xenium Explorer subset) file. The subset bundle contains the experiment.xenium, gene_panel.json, morphology_focus/ directory of multi-file OME-TIFF files, analysis_summary.html, cells.zarr.zip, cell_feature_matrix.zarr.zip, transcripts.zarr.zip, and analysis.zarr.zip files.
See the Getting Started with Xenium Explorer page for more details. Follow these instructions to view the post-Xenium H&E image or image alignment file in Xenium Explorer.
Biomaterials
Fresh frozen tissue arrays made in-house from C57 mice (male, 8 weeks old) purchased from Charles River Laboratories.
Tissue preparation
Tissues were prepared following the Demonstrated Protocols Xenium In Situ for Fresh Frozen Tissues - Tissue Preparation Guide (CG000579) and Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization (CG000581).
Probe hybridization, washing, ligation, amplification, and cell segmentation staining were performed following the Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749).
Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).
Gene panels
The Xenium Mouse Tissue Atlassing Panel (379 genes) was pre-designed by 10x Genomics. The panel design was informed by reference data from CZ Biohub San Francisco and The Tabula Muris Consortium and has been validated in the whole mouse pup and in nine adult tissues (liver, lung, heart, skin, kidney, spleen, colon, brain, thymus).
Xenium Analyzer
The instrument run was performed following the Xenium Analyzer User Guide (CG000584). The on-instrument analysis was run with Xenium Onboard Analysis version 2.0.0.
| Metric | Colon |
|---|---|
| Median transcripts per cell | 195 |
| Cells detected | 219,797 |
| Nuclear transcripts per 100 µm² | 393.7 |
| High quality decoded transcripts detected | 68,190,447 |
| Region area (µm²) | 37,101,037 |
This dataset is licensed under the Creative Commons Attribution license.