Differential expression analysis

CB Cecilia Bergonzini
AG Alessandro Gregori
TH Tessa M. S. Hagens
VN Vera E. van der Noord
BW Bob van de Water
AZ Annelien J. M. Zweemer
BC Bircan Coban
MC Mjriam Capula
GM Giulia Mantini
AB Asia Botto
FF Francesco Finamore
IG Ingrid Garajova
LM Liam A. McDonnell
TS Thomas Schmidt
EG Elisa Giovannetti
ED Erik H. J. Danen
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Differential expression analysis was performed with R package Deseq2 (version 1.22.2) for RNA-seq data and R package Limma (version 3.38.3) for proteomics data. In all datasets, black and white cases were allowed retaining the 0 for both parental and resistant cells. For RNA-seq data, only genes having a total sample count > 10 were retained. Volcano plots were generated using R package EnhancedVolcano, principal component analysis and sample correlation analyses were performed with plotPCA function of DeSeq2 R package and pheatmap R package (version 1.0.12). Finally, the R-package ggvenn was used to count the genes significantly upregulated in common among the cell lines and between RNA-seq and proteomics datasets.

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