Aim: Assessment of mRNA expression changes in a cell line after 6 h and 24 h induction of autophagy by starvation Sample: B-lymphoblastoid cell line Awells (IHW-No. 9090) Culture conditions: 6 h in DMEM, 10% FCS, 37°C, to obtain background expression under standard culture conditions RNA isolation: TRIzol (Invitrogen) followed by RNeasy-cleanup (QIAGEN) Quality control: 2100 Bioanalyzer (Agilent), high quality RNA cDNA synthesis and labeling: Standard Affymetrix protocol, BioArray High Yield RNA Transcript Labeling Kit (ENZO) Hybridization: Standard Affymetrix EukGE-WS2v4 protocol Scanning: Affymetrix GeneChip 3000 scanner Normalization: Scaling over all probe sets, target intensity = 100
