Spatial Transcriptomics Analysis for Mouse Lung Allergy Model

Analysis for Xenium figure in Bangs et al., 2025:
Tertiary lymphoid structures support the development of allergen-specific TCF1+ progenitor CD4+ T cells

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Contents

1. inputs: Required input CSV files
2. conda_envs: YAML files to create conda environments required to run notebooks
3. initial_processing: Notebooks for initial data processing, including cell labeling and spatial zone identification
4. downstream_analysis: Notebooks for spatial hypothesis testing and plot generation

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Data Download

Data access: Currently available for download by request only.

The provided data includes:

• Xenium outputs for HDM and Flu acute and memory time points
• Processed adata object for the HDM Xenium data
• Processed CITE-seq Seurat object

Running the code:

1. Clone the repo
2. Create the required conda environments:

In cpu IDE:

• conda env create -n space2 --prefix /home/workspace/environment/space2 -f /home/workspace/spatial_tls_manuscript/conda_envs/space2_20250604.yml
• conda env create -n r_seurat --prefix /home/workspace/environment/space2 -f /home/workspace/spatial_tls_manuscript/conda_envs/r_seurat_20250604.yml

In gpu IDE:

• conda env create -n cellcharter2 --prefix /home/workspace/environment/space2 -f /home/workspace/spatial_tls_manuscript/conda_envs/cellcharter2_20250604.yml

IDE and conda environments

Below are the conda environment requirements to run each notebook.

Notebook(s)	Recommended Environment	Notes
initial_processing/01_label_prediction_scanvi.ipynb	cellcharter2 (GPU IDE)	Requires GPU environment
initial_processing/04_cellcharter.ipynb	cellcharter2 (GPU IDE)	Requires GPU environment
initial_processing/03_cd4_cite_integration.ipynb	r_seurat	R environment for Seurat processing
initial_processing/00_scRNAseq_reference.ipynb	space2 (CPU IDE)	CPU environment
initial_processing/02_label_refine.ipynb	space2 (CPU IDE)	CPU environment
downstream_analysis/00_downstream_analysis.ipynb	space2 (CPU IDE)	CPU environment
downstream_analysis/01_downstream_analysis_hypothesis-testing.ipynb	space2 (CPU IDE)	CPU environment

Zenodo DOI

https://doi.org/10.5281/zenodo.15858858