miRNA-Seq

Micro-RNA Expression

Small RNA sequencing is a standardized method to uncover expression changes of miRNA in tissue/cells of interest. Similar to RNA-seq, miRNAs are enriched, amplified and sequenced, followed by reference mapping and quantification

Challenges

MiRNAs work via base-pairing with complementary sequences within mRNA. They are short (<28 nt) and have to be clustered into families to meaningfully deal with differences.

  • Genome sequence might not be available
  • Sequence divergence to reference miRNAs due to evolutionary distance or sequencing errors
  • Multiple mature miRNAs are produced from one gene and multiple read sequences map distinct miRNAs
  • MiRNA clusters include varying sequences
  • Multiple target databases exist, that do not necessarily concur

Pipeline

Results

A) Galaxy web interface to MIRPIPE, B) Schematic depiction of a miRNA cluster, C) Distribution of counts of mature miRNA families, D) Overlap of miRNA target databases, E) Web logo of a miRNA family.