Subject: Microarray analysis of Df(3R)Tl-P Microarray analysis of Df(3R)Tl-P Shinya Yamamoto, Eric Spana, Hugo Bellen and Kevin Cook DNA samples from Df(3R)Tl-P (FBab0002666) 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(3R)Tl-P breakpoint lies within CG14554, CG14551 or dys or in a region between these genes, and lies in the range 3R:21885676..21903734 (R5) (predicted cytology: 96F10-12) based on the following evidence. The gene order at the left Df(3R)Tl-P end is CG14544 (FBgn0039407), CG14551 (FBgn0039408), dys (FBgn0039411). A sequence within dys (DM00002924, 3R:21903734..21903802 (R5)) was deleted. A sequence within CG14554 (DM00002916, 3R:21885608..21885676 (R5)) was not deleted. The status of CG14551 could not be determined unequivocally in the experiment. The right Df(3R)Tl-P breakpoint probably lies within side, CG13978 or Cyp6a18 or in a region between these genes, and lies in the range 3R:23214330..23305922 (R5) (predicted cytology: 97F8-98A2) based on the following evidence. The gene order at the right Df(3R)Tl-P end is CG3348 (FBgn0040609), CG3339 (FBgn0039510), CG3330 (FBgn0039511), CG14264 (FBgn0039512), CG6599 (FBgn0039513), CG13980 (FBgn0039514), side (FBgn0016061), CG13978 (FBgn0039518), Cyp6a18 (FBgn0039519). A sequence in side (DM00002391, 3R:23214262..23214330 (R5)) was deleted. A sequence within Cyp6a18 (DM00002393, 3R:23305922..23305990 (R5)) was not deleted. The status of CG13978 could not be determined unequivocally in the experiment. Sequences within CG3339 (DM00006738, 3R:23121428..23121496 (R5)), CG14264 (DM00002661, 3R:23166746..23166781 (R5)), CG6599 (DM00009295, 3R:23189589..23189657 (R5)) and CG13980 (DM00002396, 3R:23196359..23196393 (R5)) gave intermediate fluorescence ratios, which may reflect lower quality data in these particular hybridizations or may indicate complexity at the right end of Df(3R)Tl-P. The rest of the microarray data are consistent with genes between dys and CG3348 being deleted in Df(3R)Tl-P.
