Microarray analysis of Df(3R)BSC24
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(3R)BSC24 (FBab0029839) 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 (/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(3R)BSC24 breakpoint lies within pyd or osk or in the region between them, and lies in the range  3R:4756892..4763657  (R5) (predicted cytology: 85B7) based on the following evidence.
The gene order at the left Df(3R)BSC24 end is pyd (FBgn0003177) with  tRNA:R:85Ca  (FBgn0011966), CG9731 (FBgn0037640) and  tRNA:R:85Cb  (FBgn0053551) lying in intron, osk (FBgn0003015). A sequence within osk (DM00012797,  3R:4763657..4763725  (R5)) was deleted. A sequence within pyd to the right of  tRNA:R:85Cb  (DM00000672,  3R:4756824..4756892  (R5)) was not deleted, but pyd may have been disrupted. A sequence within CG9731 (DM00011894,  3R:4688404..4688472  (R5)) was not deleted.  tRNA:R:85Ca  and  tRNA:R:85Cb  sequences were not present on the microarray.
The right Df(3R)BSC24 breakpoint lies within Fps85D or RpL34b or in the region between them, and lies in the range  3R:5220217..5226766  (R5) (predicted cytology: 85D15) based on the following evidence.
The gene order at the left Df(3R)BSC24 end is Fps85D (FBgn0000723), Or85f (FBgn0037685), CG34117 (FBgn0083953), RpL34b (FBgn0037685), CG8132 (FBgn0037687). A sequence within Fps85D (DM00013258,  3R:5220149..5220217  (R5)) was deleted. Sequences within RpL34b (DM00011592,  3R:5226766..5226834  (R5)) and CG8132 (DM00010592,  3R:5227646..5227714  (R5)) were not deleted. CG34117 sequences were not present on the microarray and Or85f sequences hybridized poorly.
The rest of the microarray data are consistent with genes between osk and Fps85D being deleted in Df(3R)BSC24.
It is quite unlikely that Df(3R)BSC24 disrupts RpL34b. Marygold et al. (2007; FBrf0205398) presented evidence that RpL34b is likely a Minute gene, yet Df(3R)BSC24 heterozygotes do not show a Minute phenotype.
The microarray data are consistent with the Df(3R)BSC24 breakpoints mapping at or very near the insertion sites of the P{EP}EP707EP707 (FBti0016468) and P{EP}EP3243 (FBti0011415) insertions used in generating the deletion by the Hybrid Element Insertion technique (Parks et al., 2004; FBrf0179070).