RAKE microRNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA90503 | ENA |
REPOSITORIES: ENA
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Project description:MicroRNAs (miRNAs) are small regulatory RNAs, which serve fundamental biological roles across eukaryotic species. We describe a novel method for high throughput miRNA detection. The technique is termed RNA-primed, Array-based, Klenow Enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over Northern blots or other microarray-based expression profiling platforms. Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalinfixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling. Keywords = microRNA Keywords: ordered
2004-11-01 | GSE1821 | GEO
Project description:MicroRNAs (miRNAs) are small regulatory RNAs, which serve fundamental biological roles across eukaryotic species. We describe a novel method for high throughput miRNA detection. The technique is termed RNA-primed, Array-based, Klenow Enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over Northern blots or other microarray-based expression profiling platforms. Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalinfixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling. Keywords = microRNA Keywords: ordered
2010-06-05 | E-GEOD-1821 | biostudies-arrayexpress
Project description:This study investigates the predictive and prognostic values of inflammatory markers and microRNA in stage IV colorectal cancer. The expression of inflammatory markers and microRNA in plasma will be correlated with tumor location, with dietary patterns and with survival during treatment.
| 2320890 | ecrin-mdr-crc
Project description:microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis
2019-02-19 | PXD011882 | Pride
Project description:Interventions: Gold Standard:colonoscopy and pathology;Index test:Stool multi-target DNA and microRNA-135b
Primary outcome(s): Stool multi-target DNA and microRNA-135b
Study Design: Diagnostic test for accuracy
| 2681097 | ecrin-mdr-crc
Project description:We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.
2014-03-31 | GSE28139 | GEO
Project description:We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.
2014-03-31 | GSE28138 | GEO
Project description:We applied a new computational approach to predict specie-specific and conserved miRNAs, than experimentally confirmed by a modified RNA-primed Array-based Klenow Extension (RAKE) method. We identified 489 conserved and 1,178 pig-specific novel miRNAs increasing our tally of confirmed miRNAs to 1,667 novel miRNAs. In addition, RAKE allowed the identification of miRNA isoforms (isomiRs) that we demonstrated to be differentially expressed across tissues suggesting that subtle variability in isomiR expression is regulated and biologically meaningful.
2014-03-31 | GSE28137 | GEO
Project description:A battery of spliceosome-associated proteins has been identified in microRNA (miRNA) biogenesis; however, the underlying mechanisms remain elusive. The intron lariat spliceosome (ILS) complex is highly conserved among eukaryotes and its disassembly marks the end of a canonical splicing cycle. In this study, we show that two conserved disassembly factors of the ILS complex, ILP1 and NTR1, positively regulate microRNA biogenesis through facilitating transcriptional elongation in Arabidopsis. ILP1 and NTR1 form a stable complex and co-regulate alternative splicing of more than a hundred genes across the genome including the core circadian gene LHY and some pri-miRNAs. Dysfunction in either ILP1 or NTR1 result in reduced RNA polymerase II occupancy at elongated regions of MIR chromatins, without affecting MIR promoter activity, pri-miRNA decay and DCL1 processing. Our results provide insights into the molecular mechanisms of spliceosomal machineries in non-coding RNA regulation.
2019-11-12 | PXD011542 | Pride
Project description:MicroRNA expression in primates II
| PRJEB2728 | ENA