human-meninges-development

Supplementary code and data to our study of the developing human meninges by Vinsland et al. (manuscript in preparation).

Preprint (bioRxiv)

(https://www.biorxiv.org/content/10.1101/2025.07.08.663122v1)

Browser

Visualizations of the complete dataset, as well as cell type specific subsets ("Superclasses"), are browsable at CELLxGENE.

Data availability

Raw sequence reads

• BAM files will be available from the European Genome/Phenome Archive (https://ega-archive.org/) under accession number TBA.

Expression matrices (scRNA-seq and spatial data)

• Complete count matrices (gene x cell counts) for the developing meninges and meningiomas are available as loom files here.
• The datasets can also be downloaded as .h5ad files from the browser: CELLxGENE.

Xenium spatial data

• Raw Xenium data and images have been deposited at the BioImage Archive under accession number S-BIAD1600.
• Complete count matrices (gene x cell counts) for meningiomas are available as loom files here.

Code used for analysis and visualisation

• Clustering was performed using the cytograph-dev version of cytograph. This is the version used for our adult human brain project. Its installation and usage are described here.
• Jupyter notebooks used to make figures are available here. The notebooks also import from cytograph-dev. (cytograph-shoji will not work).
• Jupyter notebooks used for Xenium data processing are found here.
• LDA models for topic modelling: model.bin cells.txt.