Subject: Microarray analysis of Df(2L)Prl 
Microarray analysis of Df(2L)Prl
Shinya Yamamoto, Eric Spana, Hugo Bellen and Kevin Cook
DNA samples from Df(2L)Prl (FBab0001522) 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 <http://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.
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The left Df(2L)Prl breakpoint lies in salm, sala or CG6488 or in a region between the genes, and lies in the range  2L:11437223..11497070  (R5) (predicted cytology: 32F1-2) based on the following evidence.
The gene order at the left Df(2L)Prl end is salr (FBgn0000287), salm (FBgn0004579), sala (FBgn0003313), CG6488 (FBgn0032361). A sequence from CG6488 (DM00009200,  2L:11497070..11497138  (R5)) was deleted. A sequence from salm (DM00009177,  2L:11437155..11437223  (R5)) was not deleted, but salm may have been disrupted. The status of sala could not be determined unequivocally in the experiment. A sequence from salr (DM00007894,  2L:11372854..11372895  (R5)) was not deleted.
The right Df(2L)Prl breakpoint lies within nub proximal to or within ref2, and lies in the range  2L:12614220..12626238  (R5) (predicted cytology: 33F1-2) based on the following evidence.
The gene order at the right Df(2L)Prl end is bun (FBgn0259176), nub (FBgn0085424) with ref2 (FBgn0032439) in an intron, CG12567 (FBgn0039958). Two sequences from nub (DM00003795,  2L:12594231..12594299  (R5) and DM00003794,  2L:12614152..12614220  (R5)) and a sequence from ref2 (DM00004383,  2L:12610761..12610829  (R5)) were deleted, but a more proximal sequence from nub (DM00008992,  2L:12626238..12626306  (R5)) was not deleted. A sequence from bun (DM00017240,  2L:12482561..12482615  (R5)) was deleted. A sequence from CG12567 (DM00001154,  2L:12655515..12655531  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG6488 and bun being deleted by Df(2L)Prl.
In addition to the medial 2L deletion, the Df(2L)Prl chromosomes sampled were deleted for genes at the tip of 2L, which have the order CG11023 (FBgn0031208), lgl (FBgn0002121), CG2657 (FBgn0031209), CG31973 (FBgn0051973), dbr (FBgn0067779). Sequences from CG11023 (DM00012889,  2L:9254..9322  (R5)), lgl (DM00014166,  2L:13580..13626  (R5) and DM00012974,  2L:18100..18168  (R5)) and CG2657 (DM00006310,  2L:22467..22535  (R5)) were deleted. Sequences from CG31973 (DM00006353,  2L:28754..28822  (R5)) and dbr (DM00000261,  2L:70827..70895  (R5)) were not deleted. Consequently, the deletion is likely a terminal deletion with its breakpoint in CG2657 or CG31973 or in the region between them. The breakpoint lies in the range  2L:22535..28754  (R5) (predicted cytology: 21B1). It is not known if all Df(2L)Prl chromosomes carry this terminal deletion.