Open Access Highly Accessed Research article

Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs

Ya-Ping Zhu12, Wei Xue12, Jin-Tu Wang12, Yu-Mei Wan1, Shao-Lin Wang3, Peng Xu1, Yan Zhang1, Jiong-Tang Li1* and Xiao-Wen Sun1*

Author Affiliations

1 The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, 100141, China

2 College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

3 Department of Psychiatry and Neurobiology Science, University of Virginia, Charlottesville, VA, 22911, USA

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BMC Genomics 2012, 13:413  doi:10.1186/1471-2164-13-413

Published: 21 August 2012

Additional files

Additional file 1:

Figure S1. The overall flow of the homology-based prediction of common carp miRNAs.

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Additional file 2:

Figure S2. Analysis of the hairpin structures of animal miRNA precursors.

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Additional file 3:

Table S1. Information of common carp miRNAs only identified by our homology-based prediction.

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Additional file 4:

Table S2. Information of common carp miRNAs identified by both our homology-based prediction and small RNA sequencing.

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Additional file 5:

Table S3. Information of common carp specific miRNAs identified by small RNA sequencing.

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Additional file 6:

Table S4. Specific miRNAs of which precursors were conserved without homologous miRNAs.

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Additional file 7:

Table S5. Primers of the selected miRNAs for PCR.

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Additional file 8:

Figure S3. PCR products of the selected miRNAs.

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Additional file 9:

Table S6. Predicted miRNA targets in common carp by TargetScan and PITA.

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Additional file 10:

Table S7. 18 miRNAs generated from the antisense strands of mRNAs.

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Additional file 11:

Figure S4. Resequencing SNP sites in five miRNAs using Sanger sequencing.

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Additional file 12:

Figure S5. Resequencing SNP sites in nine mRNA 3’UTRs using Sanger sequencing.

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Addition file 13:

Figure S6. The non-miRNA regions in five pre-miRNA loci had matched sRNA reads adjacent to miRNAs.

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Additional file 14:

Figure S7. False positive rate of the combination of TargetScan and PITA.

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Additional file 15:

Figure S8. The sequence identity among miRNAs in the same families.

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Additional file 16:

Table S8. Primers designed specifically for the selected miRNAs for RT-qPCR.

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Additional file 17:

Table S9. Primers designed specifically for the selected target for RT-qPCR.

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Additional file 18:

Table S10. Primers designed for PCR-based validation SNPsof miRNA precursors or mRNA sequences.

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