Computational protocol: Seasonal Expression of Prolactin Receptor in the Scented Gland of Male Muskrat (Ondatra zibethicus)

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Protocol publication

[…] The small RNA (sRNA) libraries for the scented gland of muskrat from breeding season (named: SGB1) and nonbreeding season (named: SGNB2) were constructed from total RNAs using the Illumina Truseq Small RNA Preparation kit (RS-930–1012, Illumina Inc., USA), and were sequenced on the Illumina GAIIx platform following the vendor’s recommended protocol at Beijing Yuanquanyike Biological Technology Co., Ltd (Beijing, China). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences, Houston, TX, USA), was utilized to analyze the sequencing data. The sRNAs were annotated by comparison with the deposited sequences in the NCBI GenBank (http://www.ncbi.nlm.nih.gov/) and the Rfam11.0 databases (http://rfam.sanger.ac.uk/). The remaining sequences were used to BLAST search against miRBase (version 20, http://www.mirbase.org/) to identify known miRNAs. Potential novel miRNAs candidates were predicted by Mireap (version 0.2, http://sourceforge.net/projects/mireap/). Potential target genes regulated by miRNAs were predicted using the miRanda (version 3.3a, http://www.microrna.org/microrna/). R software was utilized to analyze the correlation between differential expression profile of miRNAs and their targeted genes. The biological functions of miRNA-targeted gene candidates were revealed by Gene Ontology enrichment (GO, http://www.geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/) analyses. […]

Pipeline specifications

Software tools MIREAP, MiRanda
Databases microRNA.org Rfam miRBase KEGG
Application sRNA-seq analysis
Organisms Homo sapiens