Adults and embryos were kept at 28.5oC under a 14-hr-light/10-hr-dark cycle.
Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.
Biotinylated cDNA was prepared using the Ovation Biotin system kit (NeuGen) according to the manufacturer's instructions.
2.2 micrograms of labeled cDNA was hybridized to the Affymetrix zebrafish GeneChip at 45 degrees C for 18 hrs. Post-hybridization, staining, and washing were performed using a Fluidics Station 450 (Affymetrix) with protocol EukGE-WS2v4_450.
The hybridized chips were scanned by Affymetrix GeneChip Scanner 3000 and then processed with GeneChip Operating Software (GCOS).
Biological replicate 1 of 3
Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manufacturer's (Affymetrix) recommendations. GeneChip Operating Software (Affymetrix) was used to create CEL files from each experiment. Further statistical analysis was done using JMP, the statistical Discovery Software (http://www.jmp.com).