FRT-seq: amplification-free, strand-specific transcriptome sequencing

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Abstract
By using a reverse transcriptase for the bridge-amplification step on the Illumina Genome Analyzer, RNA conversion to cDNA and sequencing take place directly in the flowcell and yield highly accurate strand-specific sequences. We report an alternative approach to transcriptome sequencing for the Illumina Genome Analyzer, in which the reverse transcription reaction takes place on the flowcell. No amplification is performed during the library preparation, so PCR biases and duplicates are avoided, and because the template is poly(A)+ RNA rather than cDNA, the resulting sequences are necessarily strand-specific. The method is compatible with paired- or single-end sequencing.