Microarray analysis of Df(2R)Jp8
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(2R)Jp8 (FBab0001974) 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)Jp8 breakpoint lies within CG8405 or CG8414 or in the region between them, and lies in the range  2R:11946618..11987565  (R5) (predicted cytology: 52E1-52E4) based on the following evidence.
The gene order at the left Df(2R)Jp8 end is SP2353 (FBgn0034070), CG8405 (FBgn0034071), mir-137 (FBgn0082181), Dg (FBgn0034072), mRpL34 (FBgn0083983), CG8414 (FBgn0034073). A sequence within CG8414 (DM00010836,  2R:11987565..11987633  (R5)) was deleted. A sequence within CG8405 (DM00010830,  2R:11946550..11946618  (R5)) was not deleted, but CG8405 may have been disrupted. A sequence within SP2353 (DM00010828,  2R:11932624..11932685  (R5)) was not deleted. mir-137 and mRpL34 were not represented on the microarray and the spot for Dg showed poor hybridization.
The right Df(2R)Jp8 breakpoint lies within CG4282 or Vha44 or in the region between them, and lies in the range  2R:12212018..12224070  (R5) (predicted cytology: 53B5-53C1) based on the following evidence.
The gene order at the left Df(2R)Jp8 end is CG4282 (FBgn0034114), Vha44 (FBgn0020611), Hmgs (FBgn0010611). A sequence within CG4282 (DM00007426,  2R:12211950..12212018  (R5)) was deleted. A sequence within Vha44 (DM00014328,  2R:12224070..12224129  (R5)) was not deleted, but Vha44 may have been disrupted. A sequence within Hmgs (DM00013063,  2R:12224255..12224323  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG8414 and CG4282 being deleted in Df(2R)Jp8.