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Series GSE10686 Query DataSets for GSE10686
Status Public on May 12, 2008
Title Deep sequencing of small RNA libraries from chicken embryo
Organism Gallus gallus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in chickens we used a deep sequencing approach developed by Solexa (now Illumina Inc.). We sequenced three small RNA libraries prepared from different developmental stages of the chicken embryo (days 5, 7, and 9) to produce over 9.5 million short sequence reads. We developed a bioinformatics pipeline to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected almost all of the previously known chicken miRNAs and their respective miRNA* sequences. In addition we discovered 449 putative new chicken miRNAs. Of these, 430 miRNAs appear to be specific to the avian lineage. Another 6 new miRNAs had evidence of evolutionary conservation in at least one vertebrate species outside of the bird lineage. The remaining 13 putative miRNAs appear to represent chicken orthologs of known vertebrate miRNAs. We discovered 39 additional putative miRNA candidates originating from miRNA generating intronic sequences known as mirtrons.
Keywords: miRNA discovery, mirtrons, chicken embryo
Overall design 3 samples
Contributor(s) Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML
Citation(s) 18469162
Submission date Mar 02, 2008
Last update date May 15, 2019
Contact name Evgeny Glazov
Organization name University of Queensland
Department Diamantina Institute
Street address Ipswich Road
City Brisbane
ZIP/Postal code 4102
Country Australia
Platforms (1)
GPL10223 Illumina Genome Analyzer (Gallus gallus)
Samples (3)
GSM270187 CE5
GSM270188 CE7
GSM270189 CE9
SRA SRP003875
BioProject PRJNA107677

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