Microarray analysis of Df(2L)C144
Kim Cook, Eric Spana and Kevin Cook
DNA samples from Df(2L)C144 (FBab0022184) 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(2L)C144 breakpoint lies within CG3528 or CG3515 or in the region between them, and lies in the range  2L:2517598..2551864  (R5) (predicted cytology: 22F4) based on the following evidence.
The gene order at the left Df(2L)C144 end is oaf (FBgn0011818), CG3528 (FBgn0031430), CG3515 (FBgn0031431). A sequence within CG3515 (DM00006857,  2L:2551864..2551932  (R5)) was deleted. A sequence within CG3528 (DM00006865,  2L:2517537..2517598  (R5)) was not deleted, but CG3528 may have been disrupted. A sequence within oaf (DM00012013,  2L:2496901..2496969  (R5)) was not deleted.
The right Df(2L)C144 breakpoint lies within Rbp9, and lies in the range  2L:2955279..2961962  (R5) (predicted cytology: 23C3) based on the following evidence.
The gene order at the left Df(2L)C144 end is Rbp9 (FBgn0010263), Ts (FBgn0024920). A sequence within Rbp9 (DM00003710,  2L:2955211..2955279  (R5)) was deleted, but another sequence within Rbp9 (DM00013000, 2L: 2961962..2961996 (R5)) was not deleted, placing the breakpoint within Rbp9. A sequence within Ts (DM00006617, 2L: 2968985..2969053 (R5)) was not deleted.
The rest of the microarray data are consistent with genes between CG3515 and Rbp9 being deleted in Df(2L)C144.