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Sequencing of first-strand cDNA library reveals full-length transcriptomes

Author

Listed:
  • Saurabh Agarwal

    (University of Michigan)

  • Todd S. Macfarlan

    (Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health)

  • Maureen A. Sartor

    (University of Michigan)

  • Shigeki Iwase

    (University of Michigan)

Abstract

Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes. However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5′ and 3′ ends of RNAs, which can be attributed to second-strand cDNA synthesis. The 5′ and 3′ ends of RNA harbour crucial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sites. Here we report a novel ssRNA-seq method that does not involve second-strand cDNA synthesis, as we Directly Ligate sequencing Adaptors to the First-strand cDNA (DLAF). This novel method with fewer enzymatic reactions results in a higher quality of the libraries than the conventional method. Sequencing of DLAF libraries followed by a novel analysis pipeline enables the profiling of both 5′ ends and polyadenylation sites at near-base resolution. Therefore, DLAF offers the first genomics tool to obtain the ‘full-length’ transcriptome with a single library.

Suggested Citation

  • Saurabh Agarwal & Todd S. Macfarlan & Maureen A. Sartor & Shigeki Iwase, 2015. "Sequencing of first-strand cDNA library reveals full-length transcriptomes," Nature Communications, Nature, vol. 6(1), pages 1-12, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7002
    DOI: 10.1038/ncomms7002
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