Research article
Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics
1 College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
2 Zhengzhou Institute of Pomology, Chinese Academy of Agricultural Sciences, 11 Hanghai East Road, Zhengzhou 450009, People's Republic of China
BMC Genomics 2012, 13:122 doi:10.1186/1471-2164-13-122
Published: 29 March 2012Additional files
Additional file 1:
Size distribution of unique small RNA sequences from Amur grape.
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Additional file 2:
Identified conserved miRNAs from Amur grape.
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Additional file 3:
Predicted secondary structure of new potential miRNAs from Amur grape.
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Additional file 4:
3'RACE and 5' RACE products of Vv-miRNAs amplified by PCR shown in an ethidium bromide-stained agarose gel. Sizes of the molecular weight markers of the bottom and the second bottom bands are 50 bp and 100 bp on A, B, C and D, respectively. Lanes 1-20 are 3'RACE (A) and 5'RACE (B) products of 20 lower abundance va-miRNAs (va-miR398b, va-miR399c, va-miR828a, va-miR005, va-miR011, va-miR020, va-miR028, va-miR029, va-miR032, va-miR037, va-miR045, va-miR048, va-miR052, va-miR063, va-miR066, va-miR074, va-miR077, va-miR082, va-miR095 and va-miR098, respectively). Lanes 1'-20' are 3'RACE (C) and 5'RACE (D) products of 20 higher abundance va-miRNAs (va-miR156e, va-miR160c, va-miR162, va-miR164c, va-miR166c, va-miR169m, va-miR171c, va-miR172c, va-miR408, va-miR535a, va-miR001, va-miR007, va-miR016, va-miR018, va-miR023, va-miR046, va-miR047, va-miR049, va-miR057 and va-miR062, respectively). The sizes of 3'RACE products are about 83 bp while the size of 5'RACE products are about 57 bp.
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Additional file 5:
List of SNPs of conserved miRNAs in Amur grape.
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Additional file 6:
List of miR-LDs of conserved miRNAs in Amur grape.
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Additional file 7:
List of predicted target genes of non-conserved miRNAs identified in Amur grape.
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Additional file 8:
List of primers of miRNAs used for miR-5'RACE and miR-3'RACE.
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Additional file 9:
List of primers of va-miR-LDs used for miR-RACE.
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