Microarray analysis of Df(3L)R-G7
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(3L)R-G7 (FBab0002347) 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(3L)R-G7 breakpoint lies within R or CG12025 or in the region between them, and lies in the range  3L:1861374..1865717  (R5) (predicted cytology: 62B7) based on the following evidence.
The gene order at the left Df(3L)R-G7 end is CG12024 (FBgn0035283), R (FBgn0004636), HBS1 (FBgn0042712), CG12025 (FBgn0035285). A sequence within CG12025 (DM00000725,  3L:1865717..1865785  (R5)) was deleted. A sequence within R (DM00006014,  3L:1861306..1861374  (R5)) was not deleted, but Df(3L)R-G7 was isolated as a radiation-induced R1 revertant, suggesting that R is disrupted (see http://flybase.org/reports/FBrf0049893.html). A sequence within CG12024 (DM00000724,  3L:1857240..1857308  (R5)) was not deleted. Interestingly, a sequence within HBS1 (DM00005976,  3L:1863742..1863810  (R5)) appears duplicated.  While this may simply be noise in the data, it suggests that the distal breakpoint of Df(3L)R-G7 is associated with a complex rearrangement.
The right Df(3L)R-G7 breakpoint lies within CG32295 or msn or in the region between them, and lies in the range  3L:2526381..2557148  (R5) (predicted cytology: 62E5-62E6) based on the following evidence.
The gene order at the left Df(3L)R-G7 end is CG32295 (FBgn0260480), msn (FBgn0010909), RpL8 (FBgn0024939). A sequence within CG32295 (DM00015524,  3L:2526313..2526381  (R5)) was deleted. A sequence within msn (DM00004340,  3L:2557148..2557216  (R5)) was not deleted, but msn may have been disrupted. A sequence within RpL8 (DM00014258,  3L:2587478..2587513  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG12025 and CG32295 being deleted in Df(3L)R-G7.