Nature Methods
- 4, 87 - 93 (2007)
Published online: 12 November 2006; | doi:10.1038/nmeth946
SCALEs: multiscale analysis of library enrichmentMichael D Lynch, Tanya Warnecke & Ryan T Gill
Department of Chemical and Biological Engineering, University of Colorado, ECCH 111, Campus Box 424, Boulder, Colorado 80309, USA.
Correspondence should be addressed to Ryan T Gill rtg@colorado.edu We report a genome-wide, multiscale approach to simultaneously measure the effect that the increased copy of each gene and/or operon has on a desired trait or phenotype. The method involves (i) growth selections on a mixture of several different plasmid-based genomic libraries of defined insert sizes or SCALEs, (ii) microarray studies of enriched plasmid DNA, and a (iii) mathematical multiscale analysis that precisely identifies the relevant genetic elements. This approach allows for identification of all single open reading frames and larger multigene fragments within a genomic library that alter the expression of a given phenotype. We have demonstrated this method in Escherichia coli by monitoring, in parallel, a population of >106 genomic library clones of different insert sizes, throughout continuous selections over a period of 100 generations.
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