s described previously, respective flies were crossed to 337-Gal4 driver to allow for ubiquitous expression of the transgene. In each case, two samples of thirty-five staged three day old whole larvae progeny were used for RNA extraction and probing two separate microarray chips on the GeneChip Drosophila 2.0 Array following a standard 
Affymetrix protocol. Microarray data analysis GeneChip CEL files were generated using the Affymetrix GeneChip operating system. The CEL files are available at NCBI GEO. The open source packages in R and bioconductor were used for data analysis. The data were imported into R and after a series of pre-processing analysis, the data was normalized. The RMA normalization which has been shown to have high efficiency for Affymetrix data normalization was chosen to minimize the systematic variation in the experiment. Limma package was used for detection of differentially expressed genes by fitting a linear model to the expression data for each gene. This package fully models the Tip60 Mediates APP Induced Cell Death in the CNS were previously characterized and presence of each of these transgenes in the APP; dTip60 fly lines was confirmed using semiquantitative PCR. To determine whether Tip60 and APP functionally interact during general Drosophila development, we first expressed each of the transgenes separately at the normal physiological temperature of 25uC using GAL4 driver line 337, that induces robust PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/22202440 and ubiquitous GAL4 expression beginning during late embryogenesis and continuing into adulthood. The crosses were monitored daily to examine if the expression of the different transgenes affects development. In cases where the transgene expression induced lethality, the developmental stage at which lethality occurred was recorded. In cases where the F1 progeny progressed through normal development and eclosed, the number of flies that eclosed over a ten day period were counted. The w1118 fly line crossed to 337-GAL4 served as a control. As we previously reported, induction of Tip60E431Q for both independent lines A and B reduced fly viability to 0%, with the majority of lethality occurring during the late third instar larval stage. Moreover, ubiquitous induction of APP resulted in 60% lethality that occurred in the pupal stage, with the remaining 40% of progeny surviving only 25 days after eclosion. Coexpression of dTip60E431Q and APP using both APP; dTip60E431Q line A and APP; dTip60E431Q line B resulted in 0% viability, with lethality occurring during the early second instar larval stage. Additionally, hatching of 100% of these larvae was delayed by 2448 hours. Thus, co-expression of both APP and Tip60E431Q resulted in a much more severe developmental phenotype as it induced lethality approximately 3 days earlier in development than when compared to order NVP-BHG712 either APP or dTip60E431Q expressed alone. The genetic enhancement of lethal effects observed in the double mutants compared to when either APP or dTip60E431Q is expressed alone is indicative of a synergistic interaction between Tip60 and APP. To determine whether the genetic enhancement we observed between APP and dTip60 was dependent upon the C-terminal domain of APP that is required for interaction with dTip60, we coexpressed the dTip60E431Q transgene with APP dCT, a version of APP lacking the C-terminal domain. Ubiquitous expression of Tip60 Mediates APP Induced Cell Death in the CNS APP dCT alone with the 337-GAL4 driver at 25uC did not cause any observable
