New methods for next generation sequencing based microRNA expression profiling

BMC Genomics

Methodology Article

Henk PJ Buermans¹  Gertjan van Ommen¹  Peter AC 't Hoen¹  Johan T den Dunnen²  Yavuz Ariyurek³ 

[1] Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands;

关键词: Illumina Genome Analyzer;    Heart Tube;    miRNA Transcript;    Stage HH16;    microRNA Transcript;   

DOI  :  10.1186/1471-2164-11-716

 received in 2010-05-28, accepted in 2010-12-20,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundMicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer.ResultsHigh quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. The sample preparation and E-miR pipeline were used to identify 37 cardiac enriched microRNAs in stage 16 chicken embryos. Isomir expression profiles between the heart and embryo were highly correlated for all miRNAs suggesting that tissue or cell specific miRNA modifications do not occur.ConclusionsIn conclusion, our alternative sample preparation method can successfully be applied to generate high quality miRNA sequencing libraries for the Illumina genome analyzer.

【 授权许可】

CC BY   
© Buermans et al; licensee BioMed Central Ltd. 2010