RNA-Seq is a new protocol for the analysis of the RNA content of a cell. Here, we are primarily interested in the polyadenylated RNA content, mostly mRNAs, but there are variatons for extracting other small RNAs like microRNAs.
As a first step in the protocol only polyadenylated RNAs are extracted. The exact protocol varies mostly in the aspects of shearing the cDNA (e.g. nebulization or sonication), the strategy of amplification (before/after fragmentation ...), and the type of sequencing (i.e. single end or paired end sequencing). See below for references of publications where such data sets have been analyzed with different focuses and different sequencing platforms have been used for RNA-sequencing (1. Illumina Genome analyzer, 2. Applied Biosystems Solid, 3. Roche 454 Life Sciences).

References

1. Sultan,M.*, Schulz,M.H.*, Richard,H.*, Magen,A., Klingenhoff,A., Scherf,M., Seifert,M., Borodina,T., Soldatov,A., Parkhomchuk,D., Schmidt,D., O'Keeffe,S., Haas,S., Vingron,M., Lehrach,H., Yaspo,M.L. (2008)
   A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
   Science, 321(5891):956-960


2. Nicole Cloonan*, Alistair R R Forrest*, Gabriel Kolle*, Brooke B A Gardiner, Geoffrey J Faulkner, Mellissa K Brown, Darrin F Taylor, Anita L Steptoe, Shivangi Wani, Graeme Bethel, Alan J Robertson, Andrew C Perkins, Stephen J Bruce, Clarence C Lee, Swati S Ranade, Heather E Peckham, Jonathan M Manning, Kevin J McKernan & Sean M Grimmond
   Stem cell transcriptome profiling via massive-scale mRNA sequencing
   Nature Methods, July 2008, Volume 5, No 7, pages 613 - 619
   


3. J. CRISTOBAL VERA*, CHRISTOPHER W. WHEAT*, HOWARD W. FESCEMYER, MIKKO J. FRILANDER, DOUGLAS L. CRAWFORD, ILKKA HANSKI and JAMES H. MARDEN
   Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
   Molecular Ecology, 2008, Volume 17 Issue 7, pages 1636 - 1647