normalization data transformation protocol
Signals from scanned arrays were summarized using the RMA method. Data from E11.5 and E13.5 mice were summarized as two separate groups. ID_REF = VALUE = Log2 RMA signal
array scanning protocol
GeneChips were scanned using the Affymetrix GeneTitan system.
Following fragmentation, 5 micrograms of biotinylated cRNA was hybridized for 16 hr at 45C on an array (Affymetrix HT MG-430 PM Array Plate). GeneChips were washed and stained in the Affymetrix GeneTitan system.
Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3' IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix).
sample treatment protocol
Tissues were dissected in cold PBS, frozen in ethanol/dry ice slurry, and stored at -80 degree.
nucleic acid extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.