mRNA transcription profiles of livers and tumors from C57BL/6J mice treated with or without diethylnitrosamine (DEN) and fed either a Western-style diet (WD) or Control diet (CD)

We used RNA-seq to measure mRNA levels of livers and liver tumors from mice treated with or without the chemical carcinogen diethylnitrosamine (DEN) and fed CD or obesogenic WD, with the aim to explore how metabolism in hepatic tissues and tumors (where present) is affected by diet, carcinogen treatment and tumor development. We used the RNA-seq data for differential gene expression analysis, and for the reconstruction and constraining of genome-scale metabolic models in order to estimate metabolic changes across tissues under the various treatment conditions. Overall design: Four experimental groups: [1]: nonDEN-CD (mice not injected with DEN, fed CD); [2]: nonDEN-WD (mice not injected with DEN, fed WD); [3]: DEN-CD (mice injected with DEN, fed CD); [4] DEN-WD (mice injected with DEN, fed WD and bearing liver tumors) Five types of tissues (i-v) analyzed from groups 1-4: (i) Group [1] liver; (ii) Group [2] liver; (iii) Group [3] liver; (iv) Group [4]-Peritumoral tissue; (v) Group [4] tumor