SMALL RNA SEQUENCING


Small RNAs

miRNA, tRNA fragments (tiRNA), siRNA, piRNA

and more


Precise quantification of small RNA


MicroRNA (miRNA) is known to as a vital control mechanism. Each miRNA can control hundreds of messenger RNAs (mRNA), and a mRNA is most often under the control of several miRNAs, resulting in a finely balanced, intricate network of control. 

Gaining insight into small RNA expression signature in cells, tissue and biofluid of interest can have great impact on biomarker discovery, detection of treatment targets and insight into mechanisms involved.


While each project is unique and consequently the optimal solution varies accoring to the settings, some elements are will the be fairly consistent across most experiements. 

A complete omiics standard project for small RNA sequencing include:

The project starts with a meeting with a NGS-scientist, where your research

and material is discussed and the optimal startegy is designed. 

              - 18-40bp insert cDNA library

              - Multiple kit options available 

  • Stranded sequencing*

* Non-stranded sequencing is available, however, gives you less valuable data and while historical cheaper, the current prices are identical.

  • Platforms: NextSeq500 as standard
  • ≥10 Million reads/sample as standard
  • 75bp SE

SE: Single-end

  • Quality control - scoring of reads and adaptor removal,          incl. assessment of sequencing statistics
  • Mapping to known genome/transcriptome (alignment) including sequencing assessment/alignment statistics
  • Distribution of small RNA reads across RNA species incl. microRNA, rRNAs, tRNAs, snoRNAs and more

  • Differential expression analysis and cluster analysis (Gene expression annotation, expression pattern analysis, Hierarchical clustering analysis, PCA analysis, quantitative expression profiles)

  • Tables (.excl*

  • Publication-grade figures (.TIFF*)

  • Written report summarizing the procedure and results done by omiics
  • Follow-up meeting with PhD-level NGS-scientist from omiics discussing results, suggestions for interpretation and input on possible next step(s) 

*   Other formats are also available if requested 


Additional

options

below

Additional Bioinformatic Analysis for small RNA sequencing


  • Target mRNA prediction
  • Pathway analysis (Gene ontology (GO) analysis, Pathway enrichment analysis KEGG
  • Interaction analysis between differentially expressed mRNAs and differentially expressed miRNAs.
  • Length distribution of small RNAs
  • Prediction of novel miRNAs and their secondary structures by mirDentify and miRDeep-2 from
    unannotated small RNAs
  • Family analysis of known miRNAs
  • Predictive biomarker modelling by lasso-regression