Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms
Release date:
2025-04-17
Description:
We benchmarked five advanced spatial transcriptomics (ST) platforms: Stereo-seq v1.3, Visium HD FF, Visium HD FFPE, CosMx 6K, and Xenium 5K. These platforms were selected for their high-throughput gene capture (>5,000 genes), subcellular resolution (<=2um), and commercial availability. Samples from three treatment-naive tumors (colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer) were processed into FFPE blocks, fresh frozen blocks with OCT compound, and single-cell suspensions. Serial tissue sections were generated for consistent evaluation. For ground truth datasets, we profiled proteins from adjacent sections using CODEX and performed scRNA-seq on the same samples, enabling integrative cross-modal comparisons. Note that Visium HD FF protocol became available three months after initial sample preparation, possibly resulting in RNA degradation.
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Individuals & samples
Files
Submitter: Zeng Zexian / zexianzeng@pku.edu.cn
Organization: Peking University
Submission date: 2025-04-14
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HRA011129.xlsx