Chromosomes used in the crosses to generate this dataset were substituted into an isogenic background so that the final Dp(1;Y) stocks are suitable for experiments involving quantitative and background-sensitive phenotypes. A series of attached-XY stocks carrying defined FLP/FRT-induced inversions within the X portion of the attached-XY were created. Dp(1;Y) chromosomes were generated by irradiation of the attached-XY+inversion chromosomes. Deletion events that removed the proximal portion of the X were detected by screening for a distal X marker segregating with the Y. Duplications recovered in this manner are derived only from the region near the X tip; the use of attached-XY chromosomes carrying a series of X inversions with distal breakpoints allowed recovery of most regions of the X. Multiple Dp(1;Y) chromosomes were isolated from each attached-XY+inversion progenitor to form nested sets of duplicated segments. Using a PCR assay and primers flanking the transposon insertion sites, the irradiation-induced breakpoints of the duplicated segments were mapped to the resolution of regions between adjacent transgenic transposon insertion sites.

Using 22420000 as the total number of base pairs in X euchromatin, we calculated the minimal euchromatic coverage of the X chromosome provided by these duplications as 97.0%. Three coverage gaps remain.