UNIT 4.17 Quantification of microRNA Expression with Next-Generation Sequencing

  1. Seda Eminaga1,4,
  2. Danos C. Christodoulou1,4,
  3. Francois Vigneault1,2,3,4,
  4. George M. Church1,2,
  5. J.G. Seidman1

Published Online: 1 JUL 2013

DOI: 10.1002/0471142727.mb0417s103

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Eminaga, S., Christodoulou, D. C., Vigneault, F., Church, G. M. and Seidman, J. 2013. Quantification of microRNA Expression with Next-Generation Sequencing. Current Protocols in Molecular Biology. 103:II:4.17:4.17.1–4.17.14.

Author Information

  1. 1

    Department of Genetics, Harvard Medical School, Boston, Massachusetts

  2. 2

    Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts

  3. 3

    Ragon Institute of MGH, MIT, and Harvard, Charlestown, Massachusetts

  4. 4

    These authors contributed equally to this work

Publication History

  1. Published Online: 1 JUL 2013
  2. Published Print: JUL 2013


Rapid advancement of next-generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step-by-step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. Also described is a custom computational pipeline for analyzing the multiplexed miRNA library sequencing reads generated by Illumina-based technology. Curr. Protoc. Mol. Biol. 103:4.17.1–4.17.14. © 2013 by John Wiley & Sons, Inc.


  • miRNA;
  • sequencing;
  • multiplex;
  • barcode;
  • bioinformatics analysis