Services Offered

Small RNA-Seq
Analysis of Small RNA Using Next-generation Sequencers


  • Thorough and quantitative analysis of small RNA such as microRNA (miRNA), which may be heavily involved in the regulation of gene expression, cell proliferation, apoptosis, differentiation and cell metabolism, and small interfering RNA (siRNA), which is involved in RNA interference.
  • Small RNA-Seq provides a wider dynamic range and a more exhaustive analysis than microarray analysis and qRT-PCR (quantitative PCR) analysis.
  • With the large volume of data generated by next-generation sequencers, it is possible to detect small RNA with low levels of expression. Also, small RNA-Seq allows the quantitative analysis of expression frequency, from highly expressed transcripts to lowly expressed ones.


Preparation of Small RNA Libraries

  • By adding specific indexes to each sample, it is possible to mix multiple samples. After sequencing them, each sample will be analyzed independently.

High-throughput Sequencing Using Illumina HiSeq 2000

Bioinformatics Analysis

  • Evaluation of the library and sequencing data
  • Mapping to a reference genome
  • Annotations using miRBase or other resources, visualization of miRNA variants, and expression analysis
  • miRNA expression analysis (comparison of expression levels between samples)

We are able to consult on a variety of issues based on RIKEN’s rich experience in analyzing small RNA.

Secondary structure analysis (CLC Genomics Workbench)

Annotation using miRBase (CLC Genomics Workbench)

Delivered data

  • Sequencing data (Base sequence information in text format following base-calling and quality assessment data)
  • Genome mapping data (All small RNA sequence information is mapped to a reference genome)
  • Annotation data (Annotations using miRBase or other resources, and visualization of miRNA variants and expression analysis)
  • Quality Report (Results of check on quality of sequence library and sequencing data)
  • Please contact us to discuss other result formats.


Developments in Small RNA Analysis Technologies by RIKEN’s OSC

RIKEN’s OSC has developed and improved a number of small RNA analysis technologies.

Library Preparation Technologies
Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing
Mitsuoki Kawano, Chika Kawazu, Marina Lizio, Hideya Kawaji, Piero Carninci, Harukazu Suzuki, and Yoshihide Hayashizaki RIKEN Omics Science Center, Yokohama,
BioTechniques 49:751-755 (October 2010) doi 10.2144/000113516
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
Michiel J.L. de Hoon, Ryan J. Taft, Takehiro Hashimoto, Mutsumi Kanamori-Katayama, Hideya Kawaji, Mitsuoki Kawano, Mami Kishima, Timo Lassmann, Geoffrey J. Faulkner, John S. Mattick, Carsten O. Daub, Piero Carninci, Jun Kawai, Harukazu Suzuki, and Yoshihide Hayashizaki
Genome Res. 2010 20: 257-264 originally published online January 5, 2010
Access the most recent version at doi:10.1101/gr.095273.109