**Overview**

Xenium In Situ Gene Expression data for adult human tonsil sections using the Xenium Human Multi-Tissue and Cancer 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`, `morphology_mip.ome.tif`, `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](/support/software/xenium-explorer/latest) page for more details. Follow [these instructions](/support/software/xenium-explorer/latest/tutorials/xe-image-alignment) to view the post-Xenium H&E image or image alignment file in Xenium Explorer.

**Biomaterials**

FFPE-preserved tissues were purchased from Avaden Biosciences (Reactive Follicular Hyperplasia, Follicular Lymphoid Hyperplasia).

**Tissue preparation**

Tissues were prepared following the _Xenium In Situ for FFPE - Tissue Preparation Handbook_ ([CG000578](/support/in-situ-gene-expression/documentation/steps/tissue-prep/xenium-in-situ-spatial-profiling-for-ffpe-%E2%80%93-tissue-preparation-guide)).

Post-instrument processing followed the Demonstrated Protocol _Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining_ ([CG000613](/support/in-situ-gene-expression/documentation/steps/assay/xenium-in-situ-gene-expression-h-e-staining)).

**Gene panels**

The [Xenium Human Multi-Tissue and Cancer Panel](/support/software/xenium-panel-designer/latest/tutorials/pre-designed-xenium-v1) (377 genes) was pre-designed by 10x Genomics. The panel design was informed using single cell RNA sequencing data curated and reprocessed for standardization by the [Human Protein Atlas](https://www.proteinatlas.org/about/assays+annotation#singlecell_rna). Genes were chosen to accurately type cells, and identify select immune, proliferation, and tumor markers, in human breast, lung, skin, liver, colon, kidney, lung cancer, and heart.

**Xenium Analyzer**

The instrument run was performed following the _Xenium Analyzer User Guide_ ([CG000584](/support/in-situ-gene-expression/documentation/instruments/xenium-analyzer/xenium-analyzer-user-guide)). The on-instrument analysis was run with Xenium Onboard Analysis version 1.9.0.

| **Metric**                             | **Reactive follicular hyperplasia** | **Follicular lymphoid hyperplasia** |
| -------------------------------------- | ----------------------------------- | ----------------------------------- |
| Median transcripts per cell            | 50                                  | 60                                  |
| Cells detected                         | 1,349,620                           | 864,388                             |
| Decoded transcripts per 100 µm²        | 125.9                               | 111.3                               |
| Total high quality decoded transcripts | 76,442,046                          | 59,177,361                          |
| Region area (µm²)                      | 80,680,119                          | 83,386,258                          |


This Tissue Preparation Handbook provides guidance on:

- Best practices for handling tissue samples and Xenium slides before and after sectioning.
- Hematoxylin and Eosin (H&E) staining to check tissue quality.
- Sectioning practice and region of interest selection.
- Sectioning of tissue samples and placement of sections on Xenium slides.
- Deparaffinization, and decrosslinking.

The Xenium Tissue Preparation Handbook is compatible with all Xenium assay applications.


Provides step-by-step guidance for preparing formalin fixed & paraffin embedded (FFPE) tissues for downstream Xenium In Situ Gene Expression. 

Our diverse panel menu of pre-validated biologically relevant targets can be customized with up to 100 additional targets. Standalone custom panels can also be designed for your specific research questions.

Expertly curated, easily customizable in situ panels

Xenium Analyzer

Powerful in situ profiling platform using curated panels, powerful visualization software, and easy-to-follow workflow.

In Situ Gene Expression

Xenium

Gene Expression

Enables subcellular profiling of 100s of RNA targets from Fresh Frozen or FFPE tissues.

Xenium In Situ for FFPE - Tissue Preparation Handbook

Panel (JSON)

Supplemental: Add-on Panel (CSV)

Supplemental: Post-Xenium H&E image (OME-TIFF)

Supplemental: H&E Image Alignment File (CSV)

Xenium Output Bundle (full)

Xenium Output Bundle (Xenium Explorer subset)

Summary

Reactive follicular hyperplasia

Follicular lymphoid hyperplasia

Xenium Onboard Analysis

Details about the algorithms and output files generated by the Xenium Onboard Analysis pipeline.

Human Tonsil Data with Xenium Human Multi-Tissue and Cancer Panel

This document provides step-by-step instructions for using the Xenium Analyzer.

For use with:

- Xenium Analyzer, PN-1000481
- Vibration Isolation Table, PN-1000531


Provides instructions for Xenium Analyzer. 

Human Tonsil Data with Xenium Human Multi-Tissue and Cancer Panel

Assess data quality

Visualize and explore data

Metric	Reactive follicular hyperplasia	Follicular lymphoid hyperplasia
Median transcripts per cell	50	60
Cells detected	1,349,620	864,388
Decoded transcripts per 100 µm²	125.9	111.3
Total high quality decoded transcripts	76,442,046	59,177,361
Region area (µm²)	80,680,119	83,386,258