Construction of a cDNA-based microarray for Drosophila melanogaster: a comparison of gene transcription profiles from SL2 and Kc167 cells

We have constructed a DNA microarray that represents approximately 6900 of the estimated 13,598 genes in the Drosophila melanogaster genome. The microarray contains 5756 target cDNAs from the Berkeley Drosophila Genome Project, 1078 cDNAs from the National Institutes of Health Drosophila testis cDNA library, and 546 gene fragments that were amplified from genomic DNA. The methods for DNA amplification and microarray manufacture are presented. Academic researchers can obtain the microarray from the Canadian Drosophila Microarray Centre. To evaluate the utility of these arrays, we compared the gene transcription profiles of two commonly used Drosophila cell lines. Analysis revealed that 5412 spot pairs gave signals consistently above the average background in Kc167 cells, whereas 5636 spot pairs met this criterion in SL2 cells. When the expression profiles of the cell lines were compared, 1437 genes displayed at least a 1.5-fold difference, and 170 genes had a threefold or greater difference between the two cell lines. In each case, with respect to Kc167 when compared with SL2 cells, the number of genes that were upregulated was nearly equal to the number of downregulated genes. This result demonstrates that despite the similar embryonic derivation of both cell lines, their transcriptional profiles are very different.