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Materials and methods Midbrain regions which contain the cerebral aqueduct were micro-dissected from hydrocephalic and control animals at 5 days of age (n = 5). After RNA extraction and purification, total RNA was subjected to PCR techniques to generate cDNA that was subsequently labeled and hybridized (one brain per array) to the Rat 230 A oligonucleotide array from Affymetrix. Hybridization intensity for each array was measured using a confocal scanner, and results were normalized and reported as fold change differences. Raw expression data were subjected to a Student's t-test as well as the Bayesian t-test, which is a method that helps control for variations resulting from small sample size. Only those transcripts passing both the fold change of 1.5 fold and t-test cut-offs (p < 0.05) were examined further.

Gene alterations associated with closure of the cerebral aqueduct in hydrocephalic H-Tx rats