Deletion-generation strategy made use of extensive collections of isogenic FRT-carrying transgenic insertion lines (FBrf0175002); used insertions of P{XP}, PBac{RB} and PBac{WH}. Isogenized chromosomes were not used for all crosses involving the Y and 4th chromosomes. Recombination between FRT elements in two insertions in the appropriate relative orientation results in deletion of the genomic region between the insertions and production of a hybrid element that contains one FRT element at the recombination point (FBrf0091061). Animals were generated that carried a heat-shock-inducible FLP recombinase gene and 2 FRT-carrying transgenic insertions in trans; these were subjected to a heat-shock regimen during larval stages. After eclosion, females were collected and crossed to appropriate males for detection of miniwhite[-] or miniwhite[+] deficiency chromosomes; isolate lines were established using isogenized balancer stocks whenever possible. Four approaches were used to verify that the expected deletion was recovered from a screen: complementation tests, polytene chromosome cytology, hybrid PCR and PCR with primers flanking transposable element insertions. For the hybrid PCR method, IPCR primers within each FRT-bearing progenitor insertion can amplify a fragment only if they are juxtaposed by FLP-mediated recombination (are within the hybrid residual element); 93% of the deletions lacking miniwhite markers were tested by this method and all gave the expected result.

A positive hybrid PCR test was used as the sole criterion for verifying only six deletions; all other deletions were also confirmed on the basis of deleted genes or sequences.