Identification of stage-specific gene expression signatures in response to retinoic acid during the neural differentiation of mouse embryonic stem cells

We analyzed gene expression profiling by an bioinformatic approach to identify the stage-specific gene sets associated with neural differentiation of mESCs. We exposed mESCs (B6G-2 cells) to titrated doses of retinoic acid (RA) for 4 days during embryoid body formation and then performed morphological analysis on day of differentiation (DoD) 8 and 29, or genomic microarray analysis on DoD 0, 2, 8 and 29. Microarray data were analyzed by clustering methods such as self-organizing map and principal component analysis. A gene network analysis for selected gene sets was then performed using Bayesian statistics to identify stage-specific gene expression signatures in response to RA. 9 total samples: 1 vehcle, 8 Retinoic acid and two or three doses of each developmental stage(Day) [Vehicle Control (0.1% dimethyl sulfoxide), estradiol (1nM and 10nM), dehydrotestosterone (1nM and 10nM) bisphenol A (1pM and 100pM), triiodothyronine (1nM and 10nM), dexamethasone (1nM and 10nM), 2,3,7,8-tetrachlorodibenzo-p-dioxin (1nM and 10nM), 4(OH)-2’3,3’4’-5’-pentachlo biphenyls (1nM and 10nM), thalidomide (100nM and 0.01mM), bis(2-ethylhexyl)phthalate (0.001mM and 0.1mM), permethrin (100nM and 0.01mM), cyclopamine (100nM and 0.01mM), methoprene acid (0.001mM and 0.1mM)]; 1 Timepoint [48 hours].