Spatial transcriptomic profiling of FFPE and frozen colorectal cancer tissues

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. Overall design: This study compares spatial transcriptomic profiles of colorectal cancer (CRC) tissues preserved using three methods: formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF). All samples were obtained from a patient with stage IV CRC to evaluate how preservation methods affect spatial whole-transcriptome measurements. Spatial gene-expression data were generated using the NanoString GeoMx platform, covering epithelial, immune, and stromal regions within each tissue type. The dataset includes 36 spatially resolved transcriptomic profiles and provides a resource for assessing consistency and data quality across different preservation approaches in CRC research.