Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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. Comparing miRNA expression profiles for whole Chicken Embryo and isolated Heart tubes at developmental stage HH16

ORGANISM(S): Gallus gallus

SUBMITTER: Henk Buermans

PROVIDER: E-GEOD-20757 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

New methods for next generation sequencing based microRNA expression profiling.

Buermans Henk P J HP Ariyurek Yavuz Y van Ommen Gertjan G den Dunnen Johan T JT 't Hoen Peter A C PA

BMC genomics 20101220

<h4>Background</h4>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 I ...[more]

PMID: 21171994

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Project description:Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or therapeutic applications. Examination of microRNA expression of cancer and matched adjacent tissues from 7 testicular germ cell tumors and 10 transitional cell carcinomas of bladder

Dataset Information

MiRNA expression profiling in embryonic chicken heart

Publications

New methods for next generation sequencing based microRNA expression profiling.

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