README.txt

Code in the folder "ODE model" is for the NRF2-p53 mechanistic model application to triple-negative breast cancer tumors from The Cancer Genome Atlas (TCGA). NRF2p53plusH2O2_DDE.m contains the ODEs and reactions for the network model, Call_NRF2p53_TCGA100sims.m performs 100 simulations (by calling NRF2p53plusH2O2_DDE.m) per TCGA tumor with different random step increases in H2O2 generation rate (simulating random bursts of oxidative stress). run_Call_NRF2p53_TCGA100sims.sh is the bash script used to distribute simulations across multiple cores of UVa's high performance computing cluster. 

Code in the folder "RNAseq analysis" pertains to the downstream analysis after raw RNA-seq alignment and transcript assembly was done in Linux (code not provided). RNA-sequencing was performed on RNA extracted from 3D spheroids (5 cell lines (MCF10A-5E shControl, shNRF2 #1, shNRF2 #2, MCF10DCIS.com shControl, shNRF2 #1), 4 biological replicates each --> 20 total samples). RNAseqanalysis_code.R includes differential expression analysis on read counts using edgeR and hierarchical clustering of TPM-normalized samples for display.