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Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

Li Qin Wei12, Long Feng Yan123 and Tai Wang12*

Author Affiliations

1 Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China

2 National Center for Plant Gene Research, 20 Nanxincun Xiangshan Haidianqu, Beijing 100093, China

3 Graduate School of Chinese Academy of Sciences, 19A Yuquanlu Shijingshanqu, Beijing 100049, China

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Genome Biology 2011, 12:R53  doi:10.1186/gb-2011-12-6-r53

Published: 16 June 2011

Additional files

Additional file 1:

All identified known miRNAs.

Format: XLS Size: 77KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Small RNA sequences perfectly matching known miRNA hairpins.

Format: TXT Size: 4MB Download file

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Additional file 3:

Small RNA sequences perfectly matching predicted novel miRNA hairpins.

Format: TXT Size: 170KB Download file

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Additional file 4:

All predicted novel miRNAs.

Format: XLS Size: 64KB Download file

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Additional file 5:

Clustering of all known miRNAs by k-means support. The six points from the left to the right in the x-axis represent uninucleate microspores (UNMs), bicellular pollen (BCP), tricellular pollen (TCP), callus cell, root and leaf, respectively; the y-axis represents the log2 value of transcripts per million.

Format: EPS Size: 2.5MB Download file

Open Data

Additional file 6:

Clustering of all novel miRNAs by k-means support. The six points from the left to the right in the x-axis represent UNM, BCP, TCP, callus cell, root and leaf, respectively; the y-axis represents the log2 value of transcripts per million.

Format: EPS Size: 876KB Download file

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Additional file 7:

Validation of miRNAs by stem-loop real-time quantitative RT-PCR.

Format: XLS Size: 32KB Download file

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Additional file 8:

Targets of all known miRNAs and novel miRNAs. (a) Kn-miRs; (b) nov-miRs.

Format: XLS Size: 354KB Download file

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Additional file 9:

Gene ontology term 'enrichment status' for targets of pollen-enriched and sporophyte-enriched known miRNAs.

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Additional file 10:

Expression profiles of known miRNAs and novel miRNAs and their targets. (a) Kn-miRs and targets; (b) nov-miRs and targets.

Format: XLS Size: 713KB Download file

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Additional file 11:

Targets cleavage by miRNAs. (a) The predicted fold-back structures of miR56 and miR58. Mature miRNA is in red. (b) Cleavage pattern of targets by corresponding novel miRNAs. (c) Gel image showing 5' RACE reaction to detect the miRNA-directed cleavage. (d) Transient co-expression of miRNAs and their predicted targets in N. benthamiana leaves. As a positive known miRNA, the co-expression of osa-miR827a and its target LOC_Os04g11510 is also shown.

Format: EPS Size: 4.4MB Download file

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Additional file 12:

Predicted target fragments of novel miRNAs from degradome data.

Format: XLS Size: 37KB Download file

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Additional file 13:

Primers used in this study.

Format: XLS Size: 48KB Download file

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