D. simulans SNP discovery supplemental DNA sequence

Genomic DNA samples from a D. simulans scarlet ebony strain were sequenced to determine the genotype at a set of SNP positions interrogated by a custom D. simulans SNP chip. The custom array was designed for gene, exon and allele-specific expression assays. To enable decomposition of overall expression signal to allele-specific signal, the design incorporates probes for measurement of overall expression, exon expression and allele-specific expression. This novel design enables all three of these expression components to be estimated using a single platform. The flexibility of the design and the large number of probe sets allow the array to be used in a wide range of experimental designs, expanding the possible uses from abundance, isoforms and alleles to use in different strains and even in different species, such as D. melanogaster. Overall, 61,752 D. simulans SNP probe sets, including all possible bases, forward and reverse strands and multiple positions, were designed and an additional 18,769 3’ expression probe sets and 61,919 exon probe sets were printed on the array. This platform allows for straightforward and inexpensive multi-level analysis of gene expression.