SARS-CoV-2 infection drives local inflammation of the intestinal epithelium in immunocompromised patients with cancer

GeoMx Digital Spatial Profiling is a probe-based sequencing method to detect RNA spatially in tissue. We used the GeoMx Human Whole Transcriptome Atlas (18,816 genes) to sequence our tissue samples for the three patients. The Illumina FASTQ sequence files were mapped to each sample and processed to raw counts using the GeoMx NGS pipeline with default settings. The spatially oriented transcriptomes were selected by areas or interest (AOIs) that were positively stained by PanCK and CD45. The resulting data processing and quality control were performed on each AOIs. The limit of quantification (LOQ) was set to be the geometric mean of the negative control probes multiplied by the squared standard deviation of the negative control probes. Low probe count AOIs, AOIs with less than 5% of genes above the LOQ, and genes with less than 5% of AOIs above the LOQ were removed. The counts were then normalized using variance stabilizing normalization (VSN) for subsequent analyses.