Microarray analysis of Df(2R)Px2 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(2R)Px2 (FBab0002027) heterozygotes were compared to samples from wild type flies by Comparative Genomic Hybridization microarrays at the Duke Model System Genomics Unit as described in Erickson and Spana, 2006 (http://flybase.org/reports/FBrf0193934.html). Corning CGAP slides spotted with the AROS Drosophila V1.1.1 ~70 nucleotide oligo set from Eurofins MWG Operon (www.operon.com) were used for the analysis. Most annotated genes were represented by a single oligo (denoted by a DM number). Sequences present at one copy in deletion heterozygotes are detected by lower relative fluorescence when compared to sequences present in two copies in wild type flies. The left Df(2R)Px2 breakpoint lies within CG13577 or betaTub60D or in the region between them, and lies in the range 2R:20155881..20193551 (R5) (predicted cytology: 60C4-60C6) based on the following evidence. The gene order at the left Df(2R)Px2 end is CG3376 (FBgn0034997), CG13577 (FBgn0034998), nvy(FBgn0005636), CG3394 (FBgn0034999), betaTub60D (FBgn0003888). A sequence within betaTub60D (DM00013012, 2R:20193551..20193619 (R5)) was deleted. A sequence within CG13577 (DM00002016, 2R:20155813..20155881 (R5)) was not deleted, but CG13577 may have been disrupted. A sequence within CG3376 (DM00006765, 2R:20152474..20152542 (R5)) was not deleted. There was a complicated pattern of microarray hybridization for the nvy and CG3394 genes. nvy appeared deleted, but CG3394 did not. While this may simply be noise in the data, it may reflect a complex chromosomal rearrangement associated with the proximal end of Df(2R)Px2. The right Df(2R)Px2 breakpoint lies within CG4707 or CG42360 and CG42361 or in the region between them, and lies in the range 2R:20492825..20500415 (R5) (predicted cytology: 60D9) based on the following evidence. The gene order at the left Df(2R)Px2 end is CG4707 (FBgn0035036), CG42360 (FBgn0259742) with CG42361 (FBgn0259707) lying in an inton, CG4741 (FBgn0035040) with CG3608 (FBgn0035039) lying in an intron. A sequence within CG4707 (DM00007749, 2R:20492757..20492825 (R5)) was deleted. A sequence within CG42360 and CG42361 (DM00006898, 2R:20495666..20495707 (R5)) was not deleted, but, curiously, a sequence within CG42360 to the right of CG42361 appeared duplicated. Sequences within CG3608 (DM00006920, 2R:20500415..20500483 (R5)) and genes to the right of CG3608 were not deleted. While this may also be noise in the data, it suggests that the distal end of Df(2R)Px2 is associated with a complex rearrangement. Nevertheless, the deletion extends no farther distal than CG3608. The rest of the microarray data are consistent with genes between betaTub60D and CG4707 being deleted in Df(2R)Px2.
