Comparative transcriptomic analysis of Drosophila melanogaster adult brains

We identified genes whose expression is upregulated in adult Drosophila m. brain 48h after a stab lesion by microarray analysis of RNA extracted from injured and intact wild-type brains (Oregon-R). 7-day-old adult wild-type flies (Oregon-R) were injured on the right optic lobe with a stab lesion or left non-injured (controls) and kept at 25ºC. 48h after damage, brains (with the lamina removed) were collected in chilled PBS, transferred to TRIzol and snap frozen. Experimental and control samples (25 brains each) were prepared in quadruplicates. Samples were sent to the FlyChip Drosophila functional genomics unit (Cambridge) for extraction of total RNA, reverse transcription and labeling and hybridization to Drosophila whole transcriptome long-oligonucleotide array FL003 (GEO:GPL14121). Dye-swapping (2 arrays Cy5, 2 arrays Cy2) was performed to control for bias due to dye allocation. Genes showing at least fold change of -1.3 ≤ FC ≥ 1.3 and with p-value of ≤0.05 were selected for further bioinformatic analyses. Gene ontology analyses and enrichment was performed based on STRING and networks visualized with Cytoscape. Redundancy of the GO-terms was reduced with ReviGO.