aneuploid strains were generated by sporulation of the above polyploid strains , followed by karyotype stability tests and determination as described in fig . qpcr assays were designed with primers in non - coding regions on each chromosome arm ( supplementary table 1 lists primer sequences ) . dna samples were prepared by alkaline lysis , and qpcr reactions were performed in 384-well plates using a biomek fx ( beckman coulter ) to assemble 10 l reactions and an abi 7900ht ( applied biosystems ) for cycling . equal amounts ( od600 ) of aneuploid and euploid control cultures were spotted , using the biomek fx robot , onto omnitrays containing various solid media and grown under conditions listed in supplementary table 2 . omnitrays representing three biological replicates of each tested condition were scanned on an hp scanjet 4070 desktop scanner . whole - cell lysates were prepared from 50 ml cycling yeast cultures by bead - beating . the ms / ms datasets were searched using sequest23 against a database of 11,986 sequences , consisting of 5,816 s. cerevisiae non - redundant proteins ( ncbi ) , 177 contaminants and 5,993 decoy sequences . all statistical analyses were performed in the r environment25 using standard packages and custom scripts . aneuploid strains were generated by sporulation of the above polyploid strains , followed by karyotype stability tests and determination as described in fig . qpcr assays were designed with primers in non - coding regions on each chromosome arm ( supplementary table 1 lists primer sequences ) . dna samples were prepared by alkaline lysis , and qpcr reactions were performed in 384-well plates using a biomek fx ( beckman coulter ) to assemble 10 l reactions and an abi 7900ht ( applied biosystems ) for cycling . equal amounts ( od600 ) of aneuploid and euploid control cultures were spotted , using the biomek fx robot , onto omnitrays containing various solid media and grown under conditions listed in supplementary table 2 . omnitrays representing three biological replicates of each tested condition were scanned on an hp scanjet 4070 desktop scanner . whole - cell lysates were prepared from 50 ml cycling yeast cultures by bead - beating . the ms / ms datasets were searched using sequest23 against a database of 11,986 sequences , consisting of 5,816 s. cerevisiae non - redundant proteins ( ncbi ) , 177 contaminants and 5,993 decoy sequences . all statistical analyses were performed in the r environment25 using standard packages and custom scripts .
aneuploidy , referring here to genome contents characterized by abnormal numbers of chromosomes , has been associated with developmental defects , cancer , and adaptive evolution in experimental organisms19 . 
 however , it remains unresolved how aneuploidy impacts gene expression and whether aneuploidy could directly bring phenotypic variation and improved fitness over that of euploid counterparts . in this work 
 , we designed a novel scheme to generate , through random meiotic segregation , 38 stable and fully isogenic aneuploid yeast strains with distinct karyotypes and genome contents between 1n and 3n without involving any genetic selection . through phenotypic 
 profiling under various growth conditions or in the presence of a panel of chemotherapeutic or antifungal drugs , we found that aneuploid strains exhibited diverse growth phenotypes , and some aneuploid strains grew better than euploid control strains under conditions suboptimal for the latter . using quantitative mass spectrometry - based proteomics , 
 we show that the levels of protein expression largely scale with chromosome copy numbers , following the same trend observed for the transcriptome . 
 these results provide strong evidence that aneuploidy directly impacts gene expression at both the transcriptome and proteome levels and can generate significant phenotypic variation that could bring about fitness gains under diverse conditions . 
 our findings suggest that the fitness ranking between euploid and aneuploid cells is context- and karyotype - dependent , providing the basis for the notion that aneuploidy can directly underlie phenotypic evolution and cellular adaptation .