This Article OPEN ACCESS ARTICLE Full Text Full Text (PDF) Supplemental Research Data All Versions of this Article: gr.6984908v1 18/1/172    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Torres, T. T. Articles by Schlötterer, C. Search for Related Content PubMed PubMed Citation Articles by Torres, T. T. Articles by Schlötterer, C. Social Bookmarking                   What's this?

Methods

Gene expression profiling by massively parallel sequencing

¹ Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, 1210 Vienna, Austria; ² Eurofins Medigenomix GmbH, 82152 Martinsried, Germany

Massively parallel sequencing holds great promise for expression profiling, as it combines the high throughput of SAGE with the accuracy of EST sequencing. Nevertheless, until now only very limited information had been available on the suitability of the current technology to meet the requirements. Here, we evaluate the potential of 454 sequencing technology for expression profiling using Drosophila melanogaster. We show that short (< 80 bp) and long (> 300–400 bp) cDNA fragments are under-represented in 454 sequence reads. Nevertheless, sequencing of 3' cDNA fragments generated by nebulization could be used to overcome the length bias of the 454 sequencing technology. Gene expression measurements generated by restriction analysis and nebulization for fragments within the 80- to 300-bp range showed correlations similar to those reported for replicated microarray experiments (0.83–0.91); 97% of the cDNA fragments could be unambiguously mapped to the genomic DNA, demonstrating the advantage of longer sequence reads. Our analyses suggest that the 454 technology has a large potential for expression profiling, and the high mapping accuracy indicates that it should be possible to compare expression profiles across species.

E-mail christian.schloetterer@vu-wien.ac.at; fax 43-1-250775693.

[Supplemental material is available online at www.genome.org. The EST sequences have been deposited in GenBank under accession nos. EV574767–EV600806.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6984908

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				N. C. Collins, F. Tardieu, and R. Tuberosa Quantitative Trait Loci and Crop Performance under Abiotic Stress: Where Do We Stand? Plant Physiology, June 1, 2008; 147(2): 469 - 486. [Full Text] [PDF]