Subject: Microarray analysis of Df(2R)nap9 
Microarray analysis of Df(2R)nap9
Shinya Yamamoto, Eric Spana, Hugo Bellen and Kevin Cook
DNA samples from Df(2R)nap9 (FBab0002190) 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)nap9 breakpoint lies within dpr12 or Or42b or in the region between dpr12 and Or42b, and lies in the range  2R:1685751..1740465  (R5) (predicted cytology: 41F11-42A1) based on the following evidence.
The gene order at the left Df(2R)nap9 end is Tsp42A (FBgn0033042), Or42b (FBgn0033043), dpr12 (FBgn0085414). Sequences within dpr12 (DM00010307,  2R:1740465..1740533  (R5)) were deleted. A sequence within Or42b (DM00001303,  2R:1685683..1685751  (R5)) was not deleted, but Or42b may have been disrupted. A sequence within Tsp42A (DM00002846,  2R:1683223..1683291  (R5)) was not deleted.
The right Df(2R)nap9 breakpoint likely lies within Tsp42Ec or Tsp42Ed or in the region between these genes, and lies in the range  2R:2887736..2897448  (R5) (predicted cytology: 42B2) based on the following evidence.
The gene order at the right Df(2R)nap9 end is Tsp42Ea (FBgn0029508) with Tsp42Eb (FBgn0042086) within an intron, CG30160 (FBgn0050160), Tsp42Ec (FBgn0033124), Tsp42Ed (FBgn0029507). Sequences within Tsp42Ea (DM00014316,  2R:2885122..2885188  (R5)), Tsp42Eb (DM00005384,  2R:2886379..2886447  (R5)) and Tsp42Ec (DM00001376,  2R:2887668..2887736  (R5)) were deleted. Sequences within Tsp42Ed (DM00001375,  2R:2897448..2897516  (R5)) and Tsp42Ee (DM00012190,  2R:2905068..2905131  (R5)) were not deleted. The high fluorescence ratio for a sequence within CG30160 (DM00016677,  2R:2887140..2887208  (R5)) could be a false negative, or it could indicate complexity at the right end of the aberration.