Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR). For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later. For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later. For example, NoCa1-Mock refers to cells from healthy patient 1 exposed to mock treatment. The published manuscript (NAR 32:4786, 2004) can be found at http://nar.oupjournals.org/cgi/content/abstract/32/16/4786.
Data were analyzed with Affymetrix MAS version 4.0.
Normalization -- A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
ORGANISM(S): Homo sapiens
SUBMITTER: Wan-Jen Hong
REPOSITORIES: GEO, ArrayExpress
Nucleic Acids Research 20040908 16
To understand the human response to DNA damage, we used microarrays to measure transcriptional responses of 10 000 genes to ionizing radiation (IR) and ultraviolet radiation (UV). To identify bona fide responses, we used cell lines from 15 individuals and a rigorous statistical method, Significance Analysis of Microarrays (SAM). By exploring how sample number affects SAM, we rendered a portrait of the human damage response with a degree of accuracy unmatched by previous studies. By showing how S ...[more]