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MiRNA expression profiling in embryonic chicken heart

ABSTRACT: 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. 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. Both the sample preparation and E-miR pipeline were successfully used to determine cardiac enriched microRNA expression in stage 16 chicken embryos.

ORGANISM(S): Gallus gallus

PROVIDER: GSE20757 | GEO | 2010/12/21

SECONDARY ACCESSION(S): PRJNA125045

REPOSITORIES: GEO

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miRNA expression profiling in embryonic chicken heart

Project description: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. 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. Both the sample preparation and E-miR pipeline were successfully used to determine cardiac enriched microRNA expression in stage 16 chicken embryos. Comparing miRNA expression profiles for whole Chicken Embryo and isolated Heart tubes at developmental stage HH16

2010-12-21 | E-GEOD-20757 | biostudies-arrayexpress

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