We have been using a similar approach in metagenomics and metatranscriptomics to obtain absolute gene and transcript counts, rather than proportional or 'compositional' data. This type of standardization is really critical for quantitative comparisons and for reliable gene expression data. Nice job! Our publications describing the use of an internal spike of genomic DNA (somewhat surprisingly, we also use Thermus thermophilus DNA!) and artificial transcripts include:
Satinsky, B. M., S.M. Gifford, B. C. Crump, and M. A. Moran. 2013. Use of internal standards for quantitative metatranscriptome and metagenome analysis. Methods in Enzymology 531:237-250.
Satinsky, B. M., B. C. Crump, C. B. Smith, S. Sharma, B. Zielinski, M. Doherty, J. Meng, S. Sun, P. M. Medeiros, J. H. Paul, V. J. Coles, P. L. Yager, and M. A. Moran. 2014. Microspatial gene expression patterns in the Amazon River Plume. Proceedings of the National Academy of Sciences 111:11085-11090.
Moran, M. A., B. Satinsky, S. M. Gifford, H. Luo, A. Rivers, L.-K. Chan, J. Meng, B. P. Durham, C. Shen, V. A. Varaljay, C. B. Smith, P. L. Yager, and B. M. Hopkinson. 2013. Sizing up metatranscriptomics. ISME Journal 7:237-243.
Gifford, S. M., S. Sharma, J. M. Rinta-Kanto, and M. A. Moran. 2011. Quantitative analysis of a deeply-sequenced marine microbial metatranscriptome. ISME Journal 5:461-472.
Best, Mary Ann Moran (firstname.lastname@example.org)