Microarray analysis of Df(2R)en-A
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(2R)en-A (FBab0002173) 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 (/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)en-A breakpoint lies within CG13230 or shn or in the region between them, and lies in the range  2R:7042690..7102254  (R5) (predicted cytology: 47D5-47D7) based on the following evidence.
The gene order at the left Df(2R)en-A end is CG12391 (FBgn0033581), CG13230 (FBgn0040764), shn (FBgn0003396). A sequence within shn (DM00014274,  2R:7102254..7102303  (R5)) was deleted. A sequence within CG13230 (DM00001713,  2R:7042639..7042690  (R5)) was not deleted, but CG13230 may have been disrupted. A sequence within CG12391 (DM00001015,  2R:7035397..7035465  (R5)) was not deleted.
The right Df(2R)en-A breakpoint lies within CG9005 or CG9003 or in the region between them, and lies in the range  2R:7509389..7531762  (R5) (predicted cytology: 48A3-48B2) based on the following evidence.
The gene order at the left Df(2R)en-A end is CG9005 (FBgn0033638), CG9003 (FBgn0033639), CG34228 (FBgn0085257),  tRNA:CR30254  (FBgn0050254),  tRNA:M2:48Ba  (FBgn0011915), Roc2 (FBgn0044020) with CG13198 (FBgn0033640) lying in an intron. A sequence within CG9005 (DM00011305,  2R:7509321..7509389  (R5)) was deleted. A sequence within CG9003 (DM00011303,  2R:7531762..7531830  (R5)) was not deleted, but CG9003 may have been disrupted. A sequence within Roc2 and CG13198 (DM00001685,  2R:7543199..7543267  (R5)) was not deleted. CG34228,  tRNA:CR30254  and  tRNA:M2:48Ba  sequences were not present on the microarray.
The rest of the microarray data are consistent with genes between shn and CG9005 being deleted in Df(2R)en-A.