Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing

Methods. 2012 Oct;58(2):171-87. doi: 10.1016/j.ymeth.2012.07.020. Epub 2012 Jul 23.


The characterization of post-transcriptional gene regulation by small regulatory RNAs of 20-30 nt length, particularly miRNAs and piRNAs, has become a major focus of research in recent years. A prerequisite for the characterization of small RNAs is their identification and quantification across different developmental stages, normal and diseased tissues, as well as model cell lines. Here we present a step-by-step protocol for the bioinformatic analysis of barcoded cDNA libraries for small RNA profiling generated by Illumina sequencing, thereby facilitating miRNA and other small RNA profiling of large sample collections.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Gene Expression Profiling / methods
  • Gene Library*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • MicroRNAs* / chemistry
  • MicroRNAs* / genetics
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / genetics
  • Sequence Analysis, RNA / methods
  • Specimen Handling*


  • MicroRNAs
  • RNA, Small Interfering