Subject: Microarray analysis of Df(3L)ZN47 
Microarray analysis of Df(3L)ZN47
Shinya Yamamoto, Eric Spana, Hugo Bellen and Kevin Cook
DNA samples from Df(3L)ZN47 (FBab0000006) 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 breakpoint lies in CG12027 or CG4597 or in the region between them, and lies in the range  3L:5012058..5123043  (R5) (predicted cytology: 64C4-6) based on the following evidence.
The gene order at the left Df(3L)ZN47 end is CG32232 (FBgn0052232), CG34047 (FBgn0054047), CG12027 (FBgn0035585), CG4597 (FBgn0035594). A sequence in CG4597 (DM00007655,  3L:5123043..5123111  (R5)) was deleted. A sequence in CG12027 (DM00000727,  3L:5011990..5012058  (R5)) was not deleted, but CG12027 may have been disrupted. A sequence within CG32232 (DM00015516,  3L:4994473..4994541  (R5)) was not deleted and CG34047 was not represented on the microarray.
The right Df(3L)ZN47 breakpoint lies within Prat2 or CG14820 or in the region between them, and lies in the range  3R:6888496..6907374  (R5) (predicted cytology: 65D2) based on the following evidence.
The gene order at the right Df(3L)ZN47 end is Prat2 (FBgn0041194), CG14820 (FBgn0035718), tow (FBgn0035719). A sequence within Prat2 (DM00013316,  3L:6907581..6907649  (R5)) was deleted. A sequence within CG14820 (DM00003174,  3L:6926527..6926595  (R5)) was not deleted, but CG14820 may have been disrupted. A sequence within tow (DM00003175,  3L:6941085..6941123  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG4597 and Prat2 being deleted in Df(3L)ZN47.