Processed single-cell and spatial transcriptomics Seurat objects for murine glioblastoma

Processed single-cell and spatial transcriptomics Seurat objects This Zenodo record contains analysis-ready Seurat v5 objects generated for a study of glioblastoma and its microenvironment in a murine model using single-cell and spatial transcriptomics. Raw sequencing data and primary processing outputs are available via ArrayExpress. The objects provided here were used for downstream analyses and figure generation in the accompanying manuscript. v1.1 (this version): the Visium HD data have been expanded from 2 to the 4 publication-cohort samples and are now provided as one object per sample and binning resolution (previously grouped as "healthy" / "tumor"). All four Visium HD objects were rebuilt uniformly against the same custom reference. The single-cell (Flex) and Visium v1 objects are unchanged from v1.0. Contents Single-cell RNA-seq (10x Genomics Flex) seurat_flex_raw_v1.0.rds — Single-cell RNA-seq data (10x Genomics Flex). 92,737 cells from 16 samples. seurat_flex_filtered_v1.0.rds — Processed and filtered single-cell RNA-seq (10x Genomics Flex). 64,804 cells from 16 samples. Post QC filtering, sample downsampling to balance sample groups, and per-cell UMI downsampling to mitigate differences in sequencing depth. sessionInfo_seurat_flex_v1.0.txt — R session information for the Flex object. Spatial transcriptomics (10x Visium v1) seurat_visium_v1_v1.0.rds — Processed 10x Genomics Visium v1 spatial transcriptomics data (4-sample object). sessionInfo_seurat_visium_v1_v1.0.txt — R session information for the Visium v1 object. Spatial transcriptomics (10x Visium HD) Four publication-cohort samples, each provided at two binning resolutions (8 µm and 16 µm). Objects contain the counts and log-normalized data layers and the associated tissue image / coordinates. Condition and sample identity are stored in the object metadata (sample_id, condition, bin_um). Sample Condition 8 µm 16 µm HB_hm01 healthy brain seurat_visium-hd_HB_hm01_8um_v1.1.rds seurat_visium-hd_HB_hm01_16um_v1.1.rds TP_1083 tumor, primary seurat_visium-hd_TP_1083_8um_v1.1.rds seurat_visium-hd_TP_1083_16um_v1.1.rds TP_987 tumor, primary seurat_visium-hd_TP_987_8um_v1.1.rds seurat_visium-hd_TP_987_16um_v1.1.rds TR_03d_990 tumor, irradiated (3 d post-RT) seurat_visium-hd_TR_03d_990_8um_v1.1.rds seurat_visium-hd_TR_03d_990_16um_v1.1.rds sessionInfo_seurat_visium_hd_v1.1.txt — R session information for the Visium HD objects. build-manifest_visium-hd_v1.1.csv — Machine-readable manifest of the eight Visium HD objects (sample, condition, bin size, bin and feature counts). The transgene reporter probes are retained as features Tg-hPDGFB-nHA and Tg-RFP (custom reference mm10-2020-A-rcas-genelevel). Software requirements R (4.4+) Seurat (v5) Objects can be loaded in R using: seurat.object <- readRDS("seurat_flex_filtered_v1.0.rds") hd <- readRDS("seurat_visium-hd_TP_987_8um_v1.1.rds") Version history v1.1 — Visium HD expanded to 4 publication-cohort samples (added TP_987 and TR_03d_990); all HD objects reorganized to one-per-sample and rebuilt uniformly against the custom RCAS reference. Flex and Visium v1 objects unchanged. v1.0 — Initial release: Flex (raw + filtered), Visium v1, Visium HD (healthy + tumor, 8/16 µm).