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Open Access Highly Accessed Research article

Characterization of bovine miRNAs by sequencing and bioinformatics analysis

Weiwu Jin, Jason R Grant, Paul Stothard, Stephen S Moore and Le Luo Guan*

Author Affiliations

Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada

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BMC Molecular Biology 2009, 10:90  doi:10.1186/1471-2199-10-90

Published: 16 September 2009

Additional files

Additional file 1:

Table S1- Description of 11 Small RNA libraries from bovine tissues. miRNAs include reported bovine miRNAs and orthologs of known miRNAs from other mammalian species

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Additional file 2:

Table S2 - miRNAs and miRNA hairpins identified from bovine. New bovine miRNAs identified in this study are filled in gray; miRNAs identified in this study but with a different size than those reported previous are filled in green; miRNAs not-mapped bovine genome and their hairpins listed here from human are filled in yellow.

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Additional file 3:

Table S3 - Distributions of miRNA and novel miRNA candidates in 11 bovine tissues. miRNA sequences mismatched with their genome were regarded as modification (Md) if its 3' terminal has A or U additions, or the same site of miRNA, more than 2 sequences found A to G mutation (A-G transition). Other random mismatches were considered as mutations (Mt).

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Additional file 4:

Supplemental File S1 - Hairpin structures of 29 novel bovine miRNA candidates and their corresponding vertebrate orthologs. Hairpin structure of novel bovine miRNA candidates and their corresponding vertebrate orthologs are listed together. Bovine miRNA candidates and their corresponding vertebrate orthologs are shown in uppercase. Variations between bovine miRNA candidates and vertebrate orthologs are indicated in red letters. For vertebrate orthologs, species (hsa, human; mmu, mouse; rno, rat; cfa, dog; eca, horse; gga, chicken), NCBI Accession Number, Genomic location are shown.

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Additional file 5:

Table S4 - Comparison of bovine miRNA genes with those from other three mammalian species. 1: Genes for miRNA and related miRNA counted together are highlighted in yellow; "/" means "or". 2: All miRNA genes were from miRBase 12.0 and our study. 3: Star miRNAs were not listed here.

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Additional file 6:

Table S5 - Thermodynamic stability of bovine miRNA and miRNA*. The internal stability of the initial four bases of miRNA or miRNA* (5'→3') were calculated as the delta G or delta G*, using two-state hybridization web sever (http://dinamelt.bioinfo.rpi.edu/twostate.php webcite)

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Additional file 7:

Table S6 - Thermodynamic stability of human miRNA and miRNA*. The internal stability of the initial four bases of miRNA or miRNA* (5'→3') were calculated as the delta G or delta G*, using two-state hybridization web sever http://dinamelt.bioinfo.rpi.edu/twostate.php webcite.

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Additional file 8:

Table S7 - X-linked miRNAs in bovine, mouse and human. X-linked miRNAs from bovine, mouse and human, were clustered if they were less than 5,000 bp apart on the same strand.

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