Small RNA has been shown to play critical roles in developmental timing, cell fate, tumour progression and neurogenesis. Animals, plants, and fungi contain several distinct classes of small RNA, including: microRNA (miRNA), short interfering RNA (siRNA), piwi-interacting RNA (piRNA) and siRNA RNA (rasiRNA).

The study of small RNAs with next generation sequencing is a hypothesis-neutral method; it provides a whole genome analysis of expression patterns enabling the discovery and profiling of novel RNA without the limitations and probe bias of microarrays. The small RNA analysis tools from Edge Bio are designed to facilitate trimming of sequencing reads, counting and annotating of the resulting tags using miRBase or other annotation sources and performing expression analysis of the results. The methods and tools developed are inspired by the findings and methods described in [Creighton et al., 2009], [Wyman et al., 2009], [Morin et al., 2008] and [Stark et al., 2010]. An overview follows:

• Adapter trimming and summary of trimming (i.e. reads inputs, reads after trimming, avg length of read before and after trimming, etc)
• Annotation using miRBase and other resources as requested (i.e. Ensembl, or from ncRNA.org)
• Filtering - After each round of mapping, the tags that are mapped will be removed from the list of tags that continue to the next round. This means that a tag mapping with perfect match in the first round will not be considered for the subsequent one-mismatch round of mapping.
• Tag Classification - The tags are classified into the following categories according to where they match: Mature exact, Mature super, Mature sub, Mature sub/super, Mature* exact, Mature super, Mature sub, Mature sub/super, Precursor, Other
• Expression analysis - Reads matching are counted by entry for quantitative gene expression. Data are produced in text (spreadsheet-like) format, one file per sample.
• Novel miRNA exploration - Reads are mapped back to the whole genome, matches are counted in a sliding window, showing high confidence islands of previously undescribed small RNA.

This technology provides the ability to:

• Discover novel small RNAs
• Explore small RNA biology
• Characterize differential expression profiles by sequencing and comparing small RNAs across replicates

Just for SOLiD

• Detect allele specific expression patterns
• Detect as little as 1 copy of small RNA per cell

Pricing is dependent on organism and desired project design. For further information please contact our Molecular Biology Product Manager, Catherine Mair (email: cmair@vhbio.com or tel: +44 (0)191 495 8211).