Microarray analysis of Df(2R)Np5 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(2R)Np5 (FBab0024011) 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)Np5 breakpoint lies within babo or CG8216 or in the region between them, and lies in the range 2R:4848845..4852966 (R5) (predicted cytology: 44F12-44F12) based on the following evidence. The gene order at the left Df(2R)Np5 end is Tom7 (FBgn0033357), babo (FBgn0011300), CG8216 (FBgn0033358). A sequence within CG8216 (DM00010668, 2R:4852966..4853034 (R5)) was deleted. A sequence within babo (DM00010674, 2R:4848777..4848845 (R5)) was not deleted and it is unlikely that babo is disrupted, because Konev et al. (http://flybase.org/reports/FBrf0073600.html) showed that Dp(2R)Np5 complemented babo mutations. A sequence within Tom7 (DM00015100, 2R:4839506..4839573 (R5)) was not deleted. The right Df(2R)Np5 breakpoint lies within Pdk or brp or in the region between them, and lies in the range 2R:5320669..5411775 (R5) (predicted cytology: 45D6-45E3) based on the following evidence. The gene order at the left Df(2R)Np5 end is Pdk (FBgn0017558), ced-6 (FBgn0029092), Camta (FBgn0259234) with CG33758 (FBgn0053758) and CG33757 (FBgn0053757) in introns, Wnt2 (FBgn0004360), brp (FBgn0259246). A sequence within Pdk (DM00011152, 2R:5320633..5320669 (R5)) was deleted. A sequence within brp (DM00001448, 2R:5411775..5411843 (R5)) was not deleted, but brp may have been disrupted. Another sequence within brp (DM00015387, 2R:5416134..5416202 (R5)) was not deleted. There was a complicated pattern of microarray hybridization for the ced-6, Camta and Wnt2 genes (CG33758 and CG33757 were not represented on the microarray). While this may simply be noise in the data, it suggests that the distal end of Df(2R)Np5 is associated with a complex chromosomal rearrangement. The rest of the microarray data are consistent with genes between CG8216 and Pdk being deleted in Df(2R)Np5.
