title: New methods for next generation sequencing based microRNA expression profiling.
abstract: BACKGROUND
  MicroRNAs 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.
  
  
  RESULTS
  High 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.
  
  
  CONCLUSIONS
  In conclusion, our alternative sample preparation method can successfully be applied to generate high quality miRNA sequencing libraries for the Illumina genome analyzer.
authors.affiliation: Center for Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands. h.buermans@lumc.nl
authors.forename: Henk P J
authors.initials: HP
authors.lastname: Buermans
authors.forename: Yavuz
authors.initials: Y
authors.lastname: Ariyurek
authors.forename: Gertjan
authors.initials: G
authors.lastname: van Ommen
authors.forename: Johan T
authors.initials: JT
authors.lastname: den Dunnen
authors.forename: Peter A C
authors.initials: PA
authors.lastname: 't Hoen
mesh_terms: D000818:Animals; D001483:Base Sequence; D002642:Chick Embryo; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger