Verification of a custom chip which measures abundance, isoforms and alleles in Drosophila

Analysis of differential expression using the 3’ expression module revealed 34% probe sets showed evidence for a sex bias and alternative exon sex bias was identified for 164 genes. Intriguingly, allelic imbalance was detected for 37% of 6,579 probe sets examined which contained heterozygous SNP loci. Two different isogenic strains of D. simulans, st e and C167.4 and their male and female progeny were used as the basis for the verification study. Three replicates of RNA from female and male progeny of the cross st e x C167.4 made for a total of six RNA samples. In addition, DNA was used as a control for estimating allele imbalance. Three replicates of DNA target were prepared for female st e, femaleC167.4 and the female F1 progeny of the cross st e x C167.4, for a total of 9 gDNA samples.