Open Access Research article

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

Guan-Zheng Luo1, Markus Hafner2, Zhimin Shi3, Miguel Brown2, Gui-Hai Feng1, Thomas Tuschl2, Xiu-Jie Wang1* and XiaoChing Li3*

Author Affiliations

1 State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

2 Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, 10065, USA

3 Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA

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BMC Genomics 2012, 13:727  doi:10.1186/1471-2164-13-727

Published: 26 December 2012

Additional files

Additional file 1:

A summary of small RNA sequences in 8 libraries.

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Additional file 2:

Sequences, genomic loci, and expression information of all identified miRNAs. miRNAs without genomic loci were indicated separately.

Format: XLSX Size: 64KB Download file

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Additional file 3:

Conservation status of all identified miRNAs and their expression reads.

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Additional file 4:

Genomic clusters of zebra finch miRNAs and their conservation status in other species.

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Additional file 5:

miRNA* sequences and their expression information.

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Additional file 6:

Sequences and expression of 3 miR-7*s. Mature miRNAs and corresponding miRNA*s are highlighted by red and blue, respectively.

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Additional file 7:

miRNA precursors with both 5p and 3p arms producing high abundant mature miRNAs.

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Additional file 8:

Sequence reads of tgu-miR-451 and precursor structures of the atypically generated miR-451 in zebra finch, mouse, and human.

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Additional file 9:

Expression patterns of miRNA clusters in the four tissues. (A) A heatmap was plotted according to the log2 transformed normalized reads in each tissue. (B) The relative expression of three miRNA clusters in 4 tissues.

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Additional file 10:

miRNA variants with untemplated 3′ terminal modifications.

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Additional file 11:

Summary of internal nucleotide changes observed among miRNA variants. (A) The total sequence reads of each nucleotide change type detected in all tissues. (B) The relative ratio of each nucleotide change type in each tissue sample.

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Additional file 12:

Expression information of Z chromosome-encoded miRNAs.

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Additional file 13:

Predicted target genes of tgu-miR-2954.

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Additional file 14:

Expression information of zebra finch specific miRNAs.

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Additional file 15:

Comparison with the miRNA set from the Gunaratne et al. study. Fifty-three miRNAs unique in this study are listed in the box.

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