Subject: Microarray analysis of Df(3R)M-Kx1
Microarray analysis of Df(3R)M-Kx1
Shinya Yamamoto, Eric Spana, Hugo Bellen and Kevin Cook
DNA samples from Df(3R)M-Kx1 (FBab0002601) 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)M-Kx1 breakpoint lies in CG4596 or Sodh-2 or in the region between them, and lies in the range  3R:6699495..6703853  (R5) (predicted cytology: 86C7) based on the following evidence.
The gene order at the left Df(3R)M-Kx1 end is Fdh (FBgn0011768 ), CG4596 (FBgn0037849), Sodh-2 (FBgn0022359). A sequence from Sodh-2 (DM00007700,  3R:6703853..6703921  (R5)) was deleted. A sequence from CG4596 (DM00007654,  3R:6699427..6699495  (R5)) was not deleted, but CG4596 may have been disrupted. A sequence from Fdh (DM00009294,  3R:6697035..6697103  (R5)) was not deleted.
The right breakpoint of Df(3R)M-Kx1 lies within CG10013 or CG10038 or in the region between them, and lies in the range  3R:8150560..8176137  (R5) (predicted cytology: 87B6-7) based on the following evidence.
The gene order at the right Df(3R)M-Kx1 end is CG10013 (FBgn0038012), CG10038 (FBgn0038013). A sequence from CG10013 (DM00012116,  3R:8150492..8150560  (R5)) was deleted. A sequence from CG10038 (DM00013687,  3R:8176137..8176187  (R5)) was not deleted., but CG10038 may have been disrupted.
The rest of the microarray data are consistent with genes between Sodh-2 and CG10013 being deleted in Df(3R)M-Kx1.