Psoriatic arthritis disease subtypes are phenocopied in a novel humanized murine model of psoriasis and joint inflammation

<p><em><span>Data processing and analysis</span></em></p> <p><span>Data normalization, quality control, and analysis was conducted by the UPMC Hillman Cancer Bioinformatics Services. Following the GeoMX NGS pipeline (<span>sequencing saturation 92%&plusmn;0.12% (mean&plusmn;S.E.M)), t</span>he resulting read count matrix was passed through robust QC procedure to remove ROIs of low surface area (&lt;5000 &micro;m²) or low perfect aligned reads (&lt;80%), and probes of low quality or identified as global or local outliers (fails Grubbs outlier test in &ge; 20% segments). The remaining data were back-ground subtracted and Q3 normalized to house-keeping genes. ROIs were considered positive for CD8 T cells if their CD8 memory T cell deconvolution fraction was &gt; 0 (R, spatialDecon, CellProfileLibrary; Human Adult ImmuneTumor_safeTME profile). Genes differentially expressed between groups of interest were detected using gene-wise linear modeling in R (edgeR, limma v3.50.3), with p-value adjusted for false discovery rate. Contrasts of groups were performed using&nbsp;t-tests at a significance level of 0.05.</span></p>