We passaged and plated Ire1 / and hIre1 R cells into 150-cm 2 flasks for collection of microarray samples. After a 3-d growth (at 70% confluency), we either left cells untreated or induced ER stress by adding 2 mM DTT for 6 h. We then harvested the cells and purified total RNA using TRIZOL (Invitrogen). To generate labeled samples for array hybridization, we amplified 0.5 µg RNA in a single round using the amino allyl Message-Amp II aRNA kit (Applied Biosystems). As a reference for the array hybridizations, we also amplified and labeled a pool of RNA samples from NIH-3T3, Ire1 / , and hIre1 R cells (both untreated and DTT treated). In parallel, we synthesized unlabeled cDNA from 2 µg of total RNA for qPCR measurements to confirm the array data. We repeated the entire experiment for a total of three times.