NanoString Gene Expression Analysis

A literature search was carried out to identify genes associated with AbMR.9, 10, 19, 20 A custom nCounter XT CodeSet (NanoString Technologies, Seattle, WA) was used to analyze gene expression in the FFPE samples. Quality control and normalization of raw gene expression counts were performed with nSolver Analysis Software Version 4.0 (NanoString Technologies). Default parameters for quality control flagging were used for imaging (field of view registration >75%), binding density (0.05–2.25), positive control linearity (R² value >0.95), and positive control limit of detection (0.5 fM positive control ≥2 SDs above the mean of the negative controls). Background subtraction was performed for each sample by subtracting the mean of the negative controls from all data points. nSolver Analysis Software was also used to generate agglomerative cluster heat map using the Z-Score of each gene and calculating Euclidian distance between samples.