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 ( and the Rfam11.0 databases ( The remaining sequences were used to BLAST search against miRBase (version 20, to identify known miRNAs. Potential novel miRNAs candidates were predicted by Mireap (version 0.2, Potential target genes regulated by miRNAs were predicted using the miRanda (version 3.3a, 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, and Kyoto Encyclopedia of Genes and Genomes (KEGG, analyses. […]

Pipeline specifications

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