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Spatial transcriptomic profiling of FFPE and frozen colorectal cancer tissues

ABSTRACT: This dataset contains spatial whole-transcriptome profiles from colorectal cancer (CRC) tissues preserved using formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF) methods. Samples were obtained from a patient with stage IV CRC during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Each tissue type was sectioned, stained for Pan-cytokeratin (PanCK), CD45, and SYTO13, and analyzed using the NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas panel. A total of 36 areas of illumination (AOIs) representing epithelial (PanCK⁺), immune (CD45⁺), and stromal (PanCK⁻/CD45⁻) compartments were collected. Sequencing was performed on an Illumina NovaSeq 6000 platform, and raw counts were processed using NanoString DSP Analysis Suite v3.1 and R for normalization and quality control. This dataset provides spatially resolved gene-expression information across different preservation conditions of CRC tissues to support comparative analysis and method evaluation in spatial transcriptomics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE310215 | GEO | 2025/11/17

REPOSITORIES: GEO

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