GeoMx Digital Spatial Profiler Whole-Transcriptome Sequencing of human cutaneous squamous cell carcinoma with perineural invasion

Perineural invasion (PNI) is a major route of cancer progression associated with rapid disease advancement and poor clinical outcomes, yet its underlying mechanisms remain poorly understood. Here, we present a GeoMx DSP whole-transcriptome sequencing dataset generated from human cutaneous squamous cell carcinoma samples with and without PNI. This resource captures transcriptional programs across tumor, nerve, and stroma associated regions and provides a framework for investigating tumor–microenvironment interactions and molecular pathways associated with cancer progression and PNI. GeoMx DSP whole-transcriptome sequencing data were processed using the NanoString GeoMx DSP analysis pipeline. Regions of interest were filtered based on sequencing quality metrics, including read alignment, sequencing saturation, surface area, and nuclei count. Probe-level quality control and expression filtering were then performed to remove low-quality probes and lowly expressed genes. Genes detected in at least 5% of segments were retained for downstream analysis. Finally, data were normalized using Q3 normalization across all retained targets.