normalization data transformation protocol
Raw intensity values were background-corrected and RMA-transformed (Robust Multi-array Average; RMAExpress 1.0.4) to produce natural scale expression sets. ID_REF = VALUE = RMA signal intensity
array scanning protocol
GeneChips were scanned using an Axon GenePix array scanner.
standard Affymetrix protocol
Biotinylated cRNA were prepared by in vitro transcription, according to standard protocols and using 5 ug total RNA.
nucleic acid extraction protocol
Following centrifugation, cells were mechanically disrupted using glass beads in combination with a Mini-BeadBeater 16 cell disruptor (Biospec; Bartlesvile, OK), total RNA was purified using the RNeasy Mini kit (Qiagen; Valencia, CA, USA).
Cells were struck onto YPAD solid media from frozen stocks or dissection plates, and allowed to grow at 30C for 48 hrs before colonies were inoculated into liquid synthetic complete (SC) medium. After an additional 48 hrs of growth, aliquots were transferred into fresh SC medium at a concentration of ~2 x 10^5 cells/ml and grown at 30C. Samples were harvested for RNA extraction after three days of growth.