A distinct pre-treatment immune gene signature in lentigo maligna is associated with imiquimod response
Raw Nanostring Files. Total RNA was extracted from FFPE tissue sections adjacent to sections stained by multiplex IHC, using the RNeasy® FFPE Kit (Cat. 73504, QIAGEN GmbH, Hilden, Germany). 10x10um thick sections were used per sample due to the small specimen size of each biopsy. Concentration was determined using Nanodrop™ 8000 Spectrophotometer (Thermofisher Scientific, PA) and 400ng of total RNA run on the nCounter analysis system™ (nanoString™, WA) using the PanCancer Immune Profiling Panel (nanoString™, WA) consisting of 770 genes. Files include: - Raw log2 expression matrix - Sample identifiers - Raw .RCC files - RLF file
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NanoString mRNA samples were normalized using the R package NanoStringNorm (Waggott et al., 2012) where the optimal normalization method was chosen. Differential Expression analysis and significance assessment was performed using the R package Limma (Ritchie et al., 2015). Genes classified as differentially expressed were chosen by having a p-value less than 0.05 and an absolute fold change bigger than 1.1.