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A cellular and vascular atlas of the breast tumor microenvironment with multi-resolution spatial transcriptomics

Spatial transcriptomic profiling of human breast tumors to define high endothelial venule (HEV) states associated with tertiary lymphoid structures (TLSs). Includes 10x Genomics Visium data from 40 sections (33 tumor sections from 32 tumors, one profiled in duplicate, plus 7 matched uninvolved lymph nodes) and Visium HD data from 4 tumors. We identify a stromal "primed" HEV state carrying STING-associated and adhesive programs, and a mature TLS-associated state additionally marked by lymphotoxin-β receptor signaling, perivascular CCL19/CCL21 expression, and SPP1. Together these define a candidate endothelial maturation axis linked to TLS organization.

Type: Other
Archive: European Genome-phenome Archive (EGA)

1 Dataset

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Dataset ID	Description	Technology	Samples
EGAD00001016794	Raw sequencing reads (FASTQ) and Space Ranger-aligned BAMs from 10x Genomics Visium (40 sections: 33 breast tumor, 7 matched uninvolved lymph node) and Visium HD (4 breast tumors). Space Ranger count matrices are available on GEO (GSEXXXXXX). Processed AnnData/SpatialData objects, pathology annotations, and cell type mapping results are on Zenodo (https://doi.org/10.5281/zenodo.18917100). H&E, IHC, and CytAssist images, plus corresponding alignment files, are on the BioImage Archive (https://doi.org/10.6019/S-BIAD3080).	Illumina NovaSeq 6000 Illumina NovaSeq X Plus NextSeq 2000	44