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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