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 (/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.