Decoding immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid

Spatial Transcriptomics Data from Brain Tissue of Patients with Neurological Diseases

Overview:

This dataset consists of raw spatial transcriptomics data from archived brain tissues of patients with various neurological diseases, including inflammatory disease and brain cancers such as lymphomas, brain metastases, and a glioblastoma. The data were generated as part of the study titled "Decoding immune response in leptomeningeal disease through single-cell sequencing of cerebrospinal fluid" (publication link to be added once available). In this study, we explored immune profiles in the cerebrospinal fluid (CSF) of these patients, with this dataset forming the final part of the analysis, correlating immune profiles in brain tissue with those observed in the CSF.

Data Collection:

The dataset was generated using the Xenium In Situ platform and the pre-designed Xenium Human Immuno-Oncology panel, which targets 380 genes (10x Genomics). Archived human brain tissues were selected based on quality assessments using H&E and DAPI staining of adjacent sections from the same tissue blocks. For some samples, specific regions of interest within the tissue were selected for analysis rather than processing entire sections. Detailed experimental methods are available in the associated publication.

Contents:

The dataset includes raw data only. Users should refer to the associated publication for detailed experimental protocols and to the Xenium platform documentation for technical details about file structures and data handling. Outputs are generated by the Xenium In Situ, organized into folders as produced by the platform. Users are encouraged to consult 10x Genomics'  Xenium documentation for detailed guidance on file formats and content interpretation.

Metadata:

The dataset corresponds to six patient samples, which overlap with some of the CSF cohort analyzed in the associated publication. No technical or biological replicates are included. Metadata, including sample identifiers and details about disease classification, can be found in the associated publication.

Citation and Usage:

Please cite the associated publication when using this dataset. If further details or clarifications are needed, users can contact the corresponding author via the publication.