ID_REF = VALUE = normalized intensity
The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method. The trimmed mean target intensity of each array was set to 8.
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
All mice were kept in a sterile barrier facility approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee.
Cells using the markers (CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+) were collected after sorting and placed on ice in the Trizol solution (GibcoBRL). Trizol extraction of total RNA was performed according to the manufacturer's instructions.