Confounding factors in the analysis of the transcriptome response to UV exposure in skin of wild-type and human p53-variant mice

An in-vivo experiment with UV-B exposure of the skin of nude, male mice, with and without human-derived p53 variants in their genome to investigate the cellular responses upon UV-induced DNA damage. Essentially, 4 replicate mice were used for each level of UV-exposure. For each mouse a biopsy of the skin was sampled 5-6 times at different recovery time points after UV-pulse exposure, which resulted in paired samples. In total 132 treated and 132 untreated samples were taken from 64 male mice. 264 skin biopsies were taken from 48 mice on 10 timepionts and for 3 different UV-B doses. 3 different genotypes of mice were used, Wild-type (WT; p53+/+), p5372R/72R, and p5372P/72P. Later, it was determined that eight samples came from female mice instead of male mice. Therefore, the eight samples were excluded further analyses (no processed data were generated from these arrays).