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.