Transcription profiling of mouse dermal fibroblasts upon UV irradiation in a time-, dose- and lesion-dependent manner

ABSTRACT: Each labeled cDNA sample constituted a unique combination of UV dose (2J, 4J or 8J), time point (-30min, 0h, 2h, 4h, 8h and 24h) and photoreactivation status (PR or non-PR) that defined a distinctive matrix point. All samples were hybridized to non-irradiated, non-photoreactivated MDFs of the pertinent time point. As a consequence, the net observed differences in gene expression profiles between treated and non-treated cells depicted only the time-dependent expression profiles of significant gene entries upon a 2J, 4J or 8J of UV-C irradiation and subsequent photoreactivation or not.
To allow for the estimation and removal of gene specific dye effects, all samples were reversed labeled during the total RNA reverse transcription step. A pair of self-hybridizations (dye-reversed) preceded each batch of six microarrays.
Any deviation from a ratio of 1 (centered to 0 for log ratio data) in self-hybridizations was therefore assigned to either dye effect or residual error.
Dye-reversed hybridizations were considered as technical replicates that allowed gene-specific dye effects to be averaged out during clustering while enabled us to
exclude dye-dependent variances during the ANOVA analysis. In order to assure a balanced design, the same number of technical dye-reversed replicates was used for all samples and experimental conditions.
To account for inherent experimental variation, all samples were each represented by a pool of five
(occasionally six) MDF culture dishes that were subjected under identical experimental conditions.

ORGANISM(S): Mus musculus

SUBMITTER: George Garinis 

PROVIDER: E-MEXP-117 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress