Microarray analysis of Df(3R)crb87-5 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(3R)crb87-5 (FBab0002749) 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)crb87-5 breakpoint lies within jar or Orct2 or in the region between them, and lies in the range 3R:20079039..20100787 (R5) (predicted cytology: 95F6-95F8) based on the following evidence. The gene order at the left Df(3R)crb87-5 end is CG5706 (FBgn0039175), jar (FBgn0011225), Orct2 (FBgn0086365). A sequence within Orct2 (DM00002048, 3R:20100787..20100855 (R5)) was deleted. A sequence within jar (DM00008546, 3R:20078971..20079039 (R5)) was not deleted, but jar may have been disrupted. A sequence within CG5706 (DM00008554, 3R:20076307..20076375 (R5)) was not deleted. The right Df(3R)crb87-5 breakpoint lies within CG13630 or tok or in the region between them, and lies in the range 3R:20544176..20587126 (R5) (predicted cytology: 96A18-96A20) based on the following evidence. The gene order at the left Df(3R)crb87-5 end is CG13630 (FBgn0039219), tok (FBgn0004885) with snoRNA:Me18S-C1280 (FBgn0086059) lying in an intron, tld (FBgn0003719), asp (FBgn0000140), Ast (FBgn0015591), CG13631 (FBgn0040600). A sequence within CG13630 (DM00002066, 3R:20544108..20544176 (R5)) was deleted. A sequence within Ast (DM00002069, 3R:20587126..20587194 (R5)) was not deleted, but Ast may have been disrupted. A sequence within CG13631 (DM00002067, 3R:20595262..20595330 (R5)) was not deleted. There was a complicated pattern of microarray hybridization for the tok, tld and asp gene ( snoRNA:Me18S-C1280 was not represented on the microarray). tok and tld appeared undeleted, but asp appeared deleted. While this may simply be noise in the data, it may reflect a complex chromosomal rearrangement associated with the distal end of Df(3R)crb87-5. The rest of the microarray data are consistent with genes between Orct2 and CG13630 being deleted in Df(3R)crb87-5.
