The work of Patwardhan et al. open this way: at Washington, they were bothering about the effect of each possible mutation in a promoter, one base at a time. By means of synthetic saturation mutagenesis, mutant promoters were obtained by parallel solid synthesis and then released into solution, resulting in a complex library. The trick was that each oligo in the library was designed to include a unique barcode sequence downstream of the promoter's transcription start site. One library aliquot was used in an in vitro transcription reaction to make RNA from the promoter (subsequently reversely transcribed). The second aliquot was amplified using PCR only. High-throughput illumina sequencing has been carried out and quantitative comparison between the RNA barcode and the DNA barcode was used to give a measure of promoter effectiveness in a way that seems to me more clean than our classical beta-gal normalization. Ok, at the moment the technology is applied only in vitro, but the concept is clear: next generation sequencing can help the reportergenomic community. Give me a barcode plasmid and I'm going to make the reporter mouse.
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Patwardhan, R., Lee, C., Litvin, O., Young, D., Pe'er, D., & Shendure, J. (2009). High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis Nature Biotechnology, 27 (12), 1173-1175 DOI: 10.1038/nbt.1589
another barcoding strategy was blogged on March 2008.