Microarray analysis of Df(3R)p-XT103 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(3R)p-XT103 (FBab0002842) 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)p-XT103 breakpoint lies within CG31369 either within the intronic gene Or85b or to its left in the range 3R:4245820..4336007 (R5) (predicted cytology: 85A1-2) based on the following evidence. The gene order at the left Df(3R)p-XT103 end is CG31369 (FBgn0250829) with CG31462 (FBgn0051462) and Obp85a (FBgn0037589) lying within its introns, Or85b (FBgn0037590). A sequence within Or85b (DM00015657, 3R:4336007..4336068 (R5)) was deleted. A sequence within Obp85a (DM00000502, 3R:4245752..4245820 (R5)) was not deleted, but Obp85a and CG31369 may have been disrupted. A sequence within CG31369 to the right of CG31462 (DM00016089, 3R:4224231..4224299 (R5)) was not deleted. The right Df(3R)p-XT103 breakpoint lies within CG11966, CG11967 or RagA or in a region between them, and lies in the range 3R:4778677..4809191 (R5) (predicted cytology: 85B8-C1) based on the following evidence. The gene order at the left Df(3R)p-XT103 end is CG11966 (FBgn0037645), CG11967 (FBgn0037647), RagA (FBgn0037647), CG11970 (FBgn0027503). A sequence within CG11966 (DM00000676, 3R:4778609..4778677 (R5)) was deleted. A sequence within RagA (DM00000678, 3R:4809191..4809259 (R5)) was not deleted, but RagA may have been disrupted. A sequence within CG11970 (DM00000679, 3R:4815638..4815706 (R5)) was not deleted. There was no microarray sequence representing CG11967. These mapping results agree with those of Kim-Ha et al. (/reports/FBrf0053359.html), who placed the distal endpoint of Df(3R)p-XT103 30 to 40 kb distal to osk. The rest of the microarray data are consistent with genes between Or85b and CG11966 being deleted in Df(3R)p-XT103.
