Fig. 4. Gene changes in Notch1 ablated retinae at E13.5. Retinae from wild-type and Notch1 CKO littermates were harvested at E14.5, pulsed with BrdU in vitro for 1 hour and dissociated. (A) DAPI-positive cells were scored for immunoreactivity for ß-tubulin III, 270.7 or BrdU. Two-thousand to 3000 cells were scored from two or three independent retinae for each genotype. Change in immunoreactive cells in the Notch1 CKO retinae compared with control (wild type) is statistically significant (^*P<0.05, two-tailed t-test assuming equal variances). Retinae from four wild-type and Notch1 CKO littermates were harvested at E13.5 and processed for RNA isolation and cDNA preparation. cDNA was amplified, labeled and hybridized to cDNA microarrays. (B) Scatterplot representing the ratio of gene expression in wild-type versus mutant samples (y axis) plotted against the intensity value in the mutant sample (x axis). Each spot corresponds to one gene. Any spot that lies above 1 on the y axis represents a gene that is expressed at a higher level in the wild-type tissue; conversely, any spot that lies below 1 on the x axis represents a gene that is higher in the Notch1 CKO tissue. (C,D) Selected genes expressed at a lower (C) or higher (D) level in the Notch1 CKO are summarized with gene name, Accession Number, average fold change and s.d. in a dye swap experiment. ^*Some spots on array that correspond to laboratory clones, sequences are available upon request. The complete set of microarray results are included in Data S1 in the supplementary material.