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Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon

Dong-Hoon Jeong1, Skye A Schmidt1, Linda A Rymarquis15, Sunhee Park1, Matthias Ganssmann16, Marcelo A German17, Monica Accerbi1, Jixian Zhai1, Noah Fahlgren2, Samuel E Fox38, David F Garvin4, Todd C Mockler2, James C Carrington2, Blake C Meyers1 and Pamela J Green1*

Author Affiliations

1 Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

2 Donald Danforth Plant Science Center, St Louis, MO 63132, USA

3 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97322, USA

4 USDA-ARS Plant Science Research Unit, University of Minnesota, St Paul, MN 55108, USA

5 Current address: Monsanto Company, Chesterfield, MO 63017, USA

6 Current address: IBACON GmbH, Rossdorf, Germany

7 Current address: Dow AgroSciences LLC, Portland, OR 97224, USA

8 Current address: Linfield College, McMinnville, OR 97128, USA

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Genome Biology 2013, 14:R145  doi:10.1186/gb-2013-14-12-r145

Published: 24 December 2013

Additional files

Additional file 1: Table S1:

Precursors of Brachypodium miRNAs. Table S2. Conserved and non-conserved annotated miRNAs. Table S3. miRNA targets with PARE sequences at the predicted cleavage sites. Table S4.Arabidopsis miRNA targets. Table S5. Oligomers used in this study.

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Additional file 2: Figure S1:

Predicted secondary structure of Bdi-MIR444 precursors. Figure S2. Target prediction programs identified distinct subsets of targets. Figure S3. Representative D-plots for miRNA targets at each stringency level. Figure S4. Bdi-miR2118 cleavage induces phasing. Figure S5. Bdi-miR5200 in diverse plant species. Figure S6. D-plots of AGO1 for Arabidopsis, rice and Brachypodium.

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