Fresh Frozen Mouse Brain Hemisphere with 5K Mouse Pan Tissue and Pathways Panel
In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 3.0.0
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Overview
Xenium Prime 5K In Situ Gene Expression with Cell Segmentation Staining data for mouse brain hemisphere (Fresh Frozen) using the Xenium Prime 5K Mouse Pan Tissue and Pathways 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 was purchased from Charles River Labs prior to in-house embedding in OCT (Mouse (C57BL/6) Brain, non-diseased, male, 9 weeks old).
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 Prime In Situ Gene Expression with optional Cell Segmentation Staining User Guide (CG000760).
Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).
Gene panels
The Xenium Prime 5K Mouse Pan Tissue and Pathways Panel was designed to enable comprehensive cell type and cell state identification using publicly available single cell RNA sequencing data. The panels also cover canonical signaling pathways, as well as genes relevant to developmental biology and genes that are well known in biomedical literature.
Xenium Analyzer
The instrument run was performed following the Xenium Analyzer User Guide CG000584. The on-instrument analysis was run with Xenium Onboard Analysis v3.0.0.
| Metric | Brain |
|---|---|
| Median transcripts per cell | 1,088 |
| Cells detected | 63,173 |
| Nuclear transcripts per 100 µm² | 1,692.3 |
| High quality decoded transcripts detected | 149,297,699 |
| Region area (µm²) | 33,737,853.4 |
This dataset is licensed under the Creative Commons Attribution license.