Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR069821.fastq.gz | Fastqsanger.gz | |||
| SRR069822.fastq.gz | Fastqsanger.gz | |||
| SRR069823.fastq.gz | Fastqsanger.gz |
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Project description: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
2008-05-12 | GSE10686 | GEO
Project description: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 3 samples
2008-05-11 | E-GEOD-10686 | biostudies-arrayexpress
Project description:Purpose:We have used RNA-seq to examine of differentially expressed miRNAs in chicken leg muscle of three different development stages (11 embryo ages, 16 embryo ages, and 1 day old post hatch chick).The aims of this study are characterization of miRNAs differentially expressed in different developmental stage of chicken embryo, using RNA sequence sample. Methods: On this study we used two embryonic stage and one post hatch chick leg muscle of Xinghua chicken breed. Total RNA from E11 day embryo, E16 day embryo and 1 day post hatch chick was isolated by TRIzol following the manufacturer’s protocol (Invitrogen, CA, USA). Each stages were designed two samples, and the total samples were six (three group × two sample/group) and RNA samples of six individuals were pooled with equal amounts, and then were subjected to Illumina deep sequencing. Results: After eliminating adaptor and low-quality reads, a total of 5,302,700, 6,556,747, 5,359,793, 4,213,112, 7,112,885 and 7,469,939 clean reads were obtained in group E11 (E11.1-E11.2), group E16 (E16.1-E16.2) and group P1 (P1.1–P1.2) libraries, respectively. The clean reads were aligned to the chicken genome databases, miRBase, Rfam, RepBase and mRNA. Conclusions:To assess miRNA expression during chicken embryo skeletal muscle development, we sequenced and analyzed leg muscle at 11 day embryo age, 16 day embryo age, and 1 days post hatch.
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Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
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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
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