Microarray analysis of Df(2R)AA21 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(2R)AA21 (FBab0004927) 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)AA21 breakpoint lies within CG4030 or CG9394 or in the region between them, and lies in the range 2R:16976985..17007304 (R5) (predicted cytology: 57B19-57C1) based on the following evidence. The gene order at the left Df(2R)AA21 end is Treh (FBgn0003748), CG4030 (FBgn0034585), CG34396 (FBgn0085425) with CG4038 (FBgn0011824) in an intron, king-tubby (FBgn0015721) with CG9394 (FBgn0034588) in an intron. A sequence within CG9394 (DM00011624, 2R:17007304..17007372 (R5)) was deleted. A sequence within CG4030 (DM00007240, 2R:16976934..16976985 (R5)) was not deleted, but CG4030 may have been disrupted. A sequence within Treh (DM00013283, 2R:16972008..16972076 (R5)) was not deleted. Sequences within CG4038 (DM00007245, 2R:16983590 ;16983658 (R5)) and king-tubby (DM00003949, 2R:16988146 ;16988214 (R5)) appeared duplicated. While this may simply be noise in the data, it suggests that the proximal end of Df(2R)AA21 is associated with a complex chromosomal rearrangement. The right Df(2R)AA21 breakpoint lies within Sdc or CG10496 or in the region between them, and lies in the range 2R:17282113..17386709 (R5) (predicted cytology: 57E1-57E6) based on the following evidence. The gene order at the left Df(2R)AA21 end is Sdc (FBgn0010415), Sara (FBgn0026369), Fkbp13 (FBgn0010470), CG10496 (FBgn0034631), MESK2 (FBgn0043070). A sequence within Sdc (DM00012492, 2R:17282045..17282113 (R5)) was deleted. Sequences within CG10496 (DM00012491, 2R:17386709..17386777 (R5)) and MESK2 (DM00013455, 2R:17394798..17394852 (R5)) were not deleted. These results are consistent with those of Fox and Zinn (http://flybase.org/reports/FBrf0190011.html), who mapped the distal breakpoint of Df(2R)AA21 to the Sdc gene. A sequence within Sara (DM00003961, 2R:17374142..17374210 (R5)) appeared duplicated and a sequence within CG10496 (DM00014504, 2R:17376625..17376693 (R5)) appeared deleted, but a sequence within Fkbp13 (DM00011981, 2R:17374887..17374955 (R5)) appeared to be present in normal copy number. While this may also be noise in the data, it suggests that the distal end of Df(2R)AA21 is associated with a complex rearrangement. The rest of the microarray data are consistent with genes between CG9394 and Sdc being deleted in Df(2R)AA21.
