Microarray analysis of Df(2R)H3E1
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(2R)H3E1 (FBab0024377) 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)H3E1 breakpoint lies within mtt or to the right of mtt in the range  2R:4366981..4421817  (R5) (predicted cytology: 44D1-44D2) based on the following evidence.
The gene order at the left Df(2R)H3E1 end is CG8690 (FBgn0033297), mtt (FBgn0050361), CG12780 (FBgn0033301). A sequence between mtt and CG12780 (DM00003115,  2R:4421817..4421885  (R5)) was deleted. A sequence within mtt (DM00011064,  2R:4366914..4366981  (R5)) was not deleted, but mtt may have been disrupted. A sequence within CG8690 (DM00015314,  2R:4360322..4360390  (R5)) was not deleted.
The right Df(2R)H3E1 breakpoint lies within CG8213 or CG34350 or in the region between them, and lies in the range  2R:4858050..4881316  (R5) (predicted cytology: 44F12-45A1) based on the following evidence.
The gene order at the left Df(2R)H3E1 end is CG8213 (FBgn0033359), CG34350 (FBgn0085379). A sequence within CG8213 (DM00010665,  2R:4857986..4858050  (R5)) was deleted. A sequence within CG34350 (DM00000566,  2R:4881316..4881384  (R5)) was not deleted, but CG34350 may have been disrupted. Another sequence within CG34350 (DM00010633,  2R:4883210..4883278  (R5)) was not deleted.
The rest of the microarray data are consistent with genes between mtt and CG8213 being deleted in Df(2R)H3E1.