Microarray analysis of Df(3L)pbl-X1 Kim Cook, Eric Spana and Kevin Cook DNA samples from Df(3L)pbl-X1 (FBab0002391) 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(3L)pbl-X1 breakpoint lies within CTCF or pst or in the region between them, and lies in the range 3L:7349161..7350625 (R5) (predicted cytology: 65F6-65F6) based on the following evidence. The gene order at the left Df(3L)pbl-X1 end is CTCF (FBgn0035769), pst (FBgn0035770). A sequence within pst (DM00010974, 3L:7350625..7350693 (R5)) was deleted. A sequence within CTCF (DM00017087, 3L:7349093..7349161 (R5)) was not deleted, but CTCF may have been disrupted. Another sequence within CTCF (DM00010977, 3L:7347655..7347723 (R5)) was not deleted. The right Df(3L)pbl-X1 breakpoint lies within CG7504 or mus301 or in the region between them, and lies in the range 3L:8125230..8134144 (R5) (predicted cytology: 66B7-66B8) based on the following evidence. The gene order at the left Df(3L)pbl-X1 end is CG7504 (FBgn0035842), mus301 (FBgn0002899), CG13676 (FBgn0035844). A sequence within CG7504 (DM00010068, 3L:8125162..8125230 (R5)) was deleted. A sequence within mus301 (DM00010468, 3L:8134144..8134212 (R5)) was not deleted, but Gonzalez-Reyes et al. (http://flybase.org/reports/FBrf0100046.html) showed that mus301 was disrupted. A sequence within CG13676 (DM00002109, 3L:8135880..8135948 (R5)) was not deleted. The rest of the microarray data are consistent with genes between pst and CG7504 being deleted in Df(3L)pbl-X1.
