RNA-seq in D. melanogaster carrying second (CyO) and third (TM3) balancer chromosomes

We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes, and crossed it to an isogenic wild-type "virginizer" line. Trans-heterozygous adults from the F1 generation were further crossed to the wild-type parental line to obtain the pool of N1 embryos. Allele-specific RNA-seq was used to measure changes in gene expression from both chromosomes.