Microarray analysis of Df(3R)ry615
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(3R)ry615 (FBab0002910) 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)ry615 breakpoint lies within desat1 (FBgn0086687) in the range  3R:8269381..8272656  (R5) (predicted cytology: 87B10-87B11) based on the following evidence.
A sequence within desat1 (DM00014074,  3R:8272656..8272717  (R5)) was deleted, but two other sequences within desat1 (DM00013139,  3R:8269313..82693  81 and DM00013138,  3R:8267233..8267301  (R5)) were not deleted.
The right Df(3R)ry615 breakpoint lies within mthl12 or CG8790 or in the region between them, and lies in the range  3R:9181043..9190877  (R5) (predicted cytology: 87E7-87E8) based on the following evidence.
The gene order at the left Df(3R)ry615 end is mthl12 (FBgn0045442), poly (FBgn0086371), CG8790 (FBgn0027610) with poly and CG8790 overlapping. A sequence within mthl12 (DM00016173,  3R:9180975..9181043  (R5)) was deleted. A sequence shared by poly and CG8790 (DM00013254,  3R:9190877..9190945  (R5)) was not deleted, but poly and CG8790 may have been disrupted. Another sequence shared by poly and CG8790 (DM00011973,  3R:9192489..9192557  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between desat1 and mthl12 being deleted in Df(3R)ry615.