normalization data transformation protocol
The data were analysed using Bioconductor package 'oligo' under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA. ID_REF = VALUE = RMA log2 transformed signal values.
array scanning protocol
GeneChips were scanned using the Affymetrix Gene Titan instrument with AGCC 3.0 software.
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Plates were hybridized, washed and stained in the Affymetrix Gene Titan.
Biotinylated cRNA were prepared using the 3'IVT Express Kit (Ambion) from 100ng total RNA according to the manufacturer.
Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.
nucleic acid extraction protocol
RNA was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.