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Fresh Frozen Mouse Brain Replicates

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 1.0.2

Click "Open web demo" to view our fresh frozen mouse brain Xenium Explorer demo in your browser.Learn about the demo sample biology here.
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Demonstration of gene expression profiling for fresh frozen mouse brain on the Xenium platform using the pre-designed Mouse Brain Gene Expression Panel (v1). Replicate results demonstrate the high reproducibility of data generated by the platform.

10x Genomics obtained tissue from a C57BL/6 mouse from Charles River Laboratories. Three adjacent 10µm sections were placed on the same slide. 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).

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.

Key metrics

MetricReplicate 1Replicate 2Replicate 3
Median transcripts per cell252250253
Cells detected162,033154,654158,047
Decoded transcripts per 100 µm²107.0102.1105.6
Total transcripts detected49,587,80247,093,47148,460,389
Scanned tissue area (cm²)0.630.640.61

This dataset is licensed under the Creative Commons Attribution license.