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Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

Xi Chen1, Qibin Li234, Jin Wang1, Xing Guo1, Xiangrui Jiang1, Zhiji Ren1, Chunyue Weng1, Guoxun Sun1, Xiuqiang Wang15, Yaping Liu1, Lijia Ma3, Jun-Yuan Chen15, Jun Wang3, Ke Zen1, Junfeng Zhang1* and Chen-Yu Zhang1*

Author Affiliations

1 Jiangsu Diabetes Center, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Hankou Road, Nanjing, Jiangsu 210093, PR China

2 Beijing Institute of Genomics, Chinese Academy of Sciences, Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

3 Beijing Genomics Institute, Beishan Road, Yantian District, Shenzhen 518083, PR China

4 Graduate University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, PR China

5 Nanjing Institute of Palaeontology and Geology, East Beijing Road, Nanjing, Jiangsu 210008, PR China

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Genome Biology 2009, 10:R78  doi:10.1186/gb-2009-10-7-r78

Published: 17 July 2009

Additional files

Additional data file 1:

Table S1: categories of amphioxus small RNAs. Table S2: MIREAP output. Table S3: MIREAP summary, miRAlign output and MiPred output. Table S4: mature sequences of amphioxus miRNAs and their cloning frequencies. Table S5: detailed precursor sequences and exact genome locations of all amphioxus miRNAs. Table S6: plausible amphioxus miRNAs. Table S7: comparison of miRNA expression levels in amphioxus determined by Solexa sequencing and microarray analysis. Table S8: raw data of miRNA microarray. Table S9: evolution history of amphioxus miRNAs. Table S10: comparison of miRNA identified from B. belcheri (Gray), B. floridae, and B. japonicum.

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Additional data file 2:

Predicted stem-loop structures of conserved amphioxus miRNAs.

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Additional data file 3:

Predicted stem-loop structures of amphioxus-specific miRNAs.

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Open Data