!Name=Array CGH of Drosophila compound chromosomes on heterochromatin custom array !ExptSetNo=6721 !Description=CGH analysis of embryos lacking specific chromosomes or chromosome arms. For each experiment 100-150 embryos of the appropriate genotype were collected, dechorionated and digested with proteinase K prior to phenol/chloroform extraction. DNA was then sonicated and sodium acetate/ethanol precipitated. DNA extracted from randomly staged 0-8 hr wild type Oregon R embryos was used as reference for all experiments. Purified DNA was labeled using the BioPrime kit (Life Technologies) and hybridized with the microarray following standard Agilent CGH protocol. Feature extraction was performed by Agilent feature extraction software using the CGH protocol. Embryos with no X chromosome were obtained by crossing attached-X/Y females to X/Y males. The stock used was C(1)DX, y f (Wieschaus and Sweeton, 1988). Embryos with no X and Y chromosomes were obtained by crossing attached-X/Y females (C(1)RM, y2suwawa) to attached-XY males (YSX YL, In(1)EN, y B). The compound II chromosomes RM(2L); RM(2R)=C(2)v and the compound III chromosomes RM(3L); RM(3R)=C(3)se, in which the two left arms or the two right arms segregate together, were used to generate 2L- and 2R-, and 3L- and 3R- embryos, respectively(Merrill et al., 1988). The compound II C(2)EN and compound III C(3)EN st1 cu1es, stocks (Bloomington 2974 and 1117) were used to generate embryos deficient for the entire second and third chromosome, respectively. The compound IV C(4)RM, ci1eyR/0 (Bloomington 1785) were used to generate embryos deficient for the fourth chromosome. Embryos deficient for chromosome 4 were identified by their defects in denticle belt patterning during late embryogenesis, whereas embryos deficient for other chromosome/chromosome arm were recognized based on their specific phenotypic defects during early embryonic development (Wieschaus and Sweeton, 1988; Merrill et al, 1988) . The early embryonic development phenotypes can be easily recognized by covering embryos in oil to make them transparent, and then viewing them in transmitted light under a stereomicroscope. All embryos were collected at room temperature. !Name=Chr2L- !Exptid=112437 !Name=Chr2R- repeat hybridization !Exptid=113218 !Name=Chr2entire- repeat hybridization !Exptid=113219 !Name=Chr3L- repeat hybridization !Exptid=113217 !Name=Chr3R- repeat hybridization !Exptid=113216 !Name=Chr3entire- !Exptid=113801 !Name=Chr4entire- !Exptid=113684 !Name=ChrX- repeat hybridization !Exptid=113215 !Name=ChrXY- repeat hybridization !Exptid=113214 !Name=WT (Cycle14 ORE R) !Exptid=112436