E-TABM-143 - Comparative genomic hybridization of plasmids containing genomic library clones grown in E. coli to monitor copy number changes over time

Status
Submitted on 27 August 2006, released on 26 October 2006, last updated on 10 June 2011
Organism
Escherichia coli
Samples (9)
Array (1)
Protocols (6)
Description
We report a genome-wide, multi-scale 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) micro-array studies of enriched plasmid DNA, and a ii) mathematical multi-scale analysis (MSA) that precisely identifies the relevant genetic elements. This approach allows for identification of all single open reading frames and larger multi-gene fragments within a genomic library that alter the expression of a given phenotype. We have demonstrated this method in E. 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.
Experiment type
comparative genomic hybridization by array 
Contact
Citation
SCALES: SCalar Analysis of Library Enrichments. Michael D. Lynch, Tanya Warnecked, Ryan T. Gill. Nat Methods  (2006)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-143.idf.txt
Sample and data relationshipE-TABM-143.sdrf.txt
Raw data (1)E-TABM-143.raw.1.zip
Array designA-AFFY-29.adf.txt
R ExpressionSetE-TABM-143.eSet.r
Links