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Same as genetic footprinting, only at a high throughput, systems level way. Typically you use a transposon library to insert mutations to cells that inactivate genes (you assume one transposon/inactivation per cell). Then you trascription profile (dna microarray, rna-seq) after selection (whatever you want to select for, growth, resistance etc) and try to map the mutations/genes inactivations to the fitness changes in the cells.

For example if you select for growth in a particular environment and the deletion of a gene confers this, then during selection that mutant will be over-represented, so when you run a microarray, you will see no expression of the deleted gene in reference with the wild type strain.

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Q: What is the definition of genomic footprinting?
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