Computational protocol: Acceleration of healing of the medial collateral ligament of the knee by local administration of synthetic microRNA-210 in a rat model

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Protocol publication

[…] Total RNA for DNA microarray was extracted from the repaired site in each group using TRIzol (Life Technologies, Carlsbad, California, USA), according to the manufacturer's instructions. One microgram of the total RNA was used for the DNA microarray analysis. After amplification, the RNA sample in each group (n = 1 in each group) was labelled with Cy3 or Cy5, and hybridised with 3D-Gene Rat Oligo chip 24k (Toray Industries Inc., Tokyo, Japan). After hybridisation, hybridisation signals were scanned using 3D Gene Scanner 3000 (Toray Industries Inc.), and all the data from scanned images were scaled by global normalisation. From microarray data, the differentially expressed genes during MCL healing were analysed by gene ontology and pathway enrichment analysis. Gene ontology analysis was performed using GeneCodis2.0 software to integrate differentially expressed genes and to evaluate groups of genes with similar biological function., , GenMAPP (gene map annotator and pathway profiler), which allows us to view and analyse microarray data on biological pathways, was also used to identify which pathways are affected by miR-210 during MCL healing. […]

Pipeline specifications

Software tools GeneCodis, GenMAPP
Application Gene expression microarray analysis
Organisms Rattus norvegicus