Microarray analysis of Df(3R)D605
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(3R)D605 (FBab0002515) 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(3R)D605 breakpoint lies within CG14258 or CG14259 or in the region between them, and lies in the range  3R:22919628..22921324  (R5) (predicted cytology: 97E2) based on the following evidence.
The gene order at the left Df(3R)D605 end is Cpr97Eb (FBgn0039481), CG14258 (FBgn0039482), CG14259 (FBgn0039483). A sequence within CG14259 (DM00002656,  3R:22921324..22921392  (R5)) was deleted. A sequence within CG14258 (DM00002655,  3R:22919560..22919628  (R5)) was not deleted, but CG14258 may have been disrupted. A sequence within Cpr97Eb (DM00004123,  3R:22916151..22916219  (R5)) was not deleted.
The right Df(3R)D605 breakpoint lies within CG13972 or CG12885 or in the region between them, and lies in the range  3R:23342311..23358483  (R5) (predicted cytology: 98A3-98A4) based on the following evidence.
The gene order at the left Df(3R)D605 end is CG13972 (FBgn0039522), CG12885 (FBgn0039523), Gr98b (FBgn0046887). A sequence within CG13972 (DM00002388,  3R:23342243..23342311  (R5)) was deleted. A sequence within CG12885 (DM00001412,  3R:23358483..23358551  (R5)) was not deleted, but CG12885 may have been disrupted. A sequence within Gr98b (DM00015169,  3R:23369292..23369338  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG14259 and CG13972 being deleted in Df(3R)D605.