A distinct pre-treatment immune gene signature in lentigo maligna is associated with imiquimod response

Published: 3 April 2019| Version 2 | DOI: 10.17632/2cc3yvvzk4.2
Heloise Halse, Simon Keam


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.


Peter MacCallum Cancer Institute


Gene Expression