Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation

Jackson-Grusby, L. et al. Nature Genet. 27, 31-39 (2001)

This site supplies additional data supporting our paper. The entire 2.2Mb Dnmt1 microarray dataset can be downloaded as a tab-separated value (tsv) file that can be opened in Microsoft Excel.

For convenience, we are providing the globally scaled data, however the data are not floored to allow the user more flexibility for analysis. The first two columns include the descriptions and accession numbers for the analyzed genes. There are 32 columns containing data. Each RNA sample analyzed is described by two columns of information: the expression signal and the confidence measure. The expression is calculated as an averaged difference between twenty perfect match oligos and the internal mismatch oligo controls, therefore not all values are positive numbers. We have set all values below 50 to 50 for the analysis in our paper. The confidence measure is a statistical calculation made by the Affymetrix software that indicates high confidence (P), no call of confidence (M), low/no confidence (A). The "P" calls are an approximate measure of presence of expression and the "A" calls generally mean the gene is absent or not expressed.

We analyzed expression from four T antigen transformed Dnmt1 conditional cell lines infected with a Cre retrovirus (Mutant 1-4) or the puro control retrovirus (Control 1-4). We also analyzed expression from four p53 mutant Dnmt1 conditional primary mouse embryonic fibroblasts infected with a Cre retrovirus (Mutant 5-8) or the puro control retrovirus (Control 5-8).

For questions regarding the dataset or website, contact Laurie Jackson-Grusby: jackson@wi.mit.edu.