Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray

Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-ba...

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Published in:Journal of Nucleic Acids 2012-01, Vol.2012 (2012), p.124-133
Main Authors: Skreka, Konstantinia, Zywicki, Marek, Karbiener, Michael, Hüttenhofer, Alexander, Scheideler, Marcel, Rederstorff, Mathieu
Format: Article
Language:English
Subjects:
Biochemistry, Molecular Biology
Biomarkers
Deoxyribonucleic acid
DNA
Genes
Genomes
Hybridization
Labeling
Life Sciences
Protocol
Stem cells
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creator Skreka, Konstantinia
Zywicki, Marek
Karbiener, Michael
Hüttenhofer, Alexander
Scheideler, Marcel
Rederstorff, Mathieu
description Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-based technologies for high-throughput expression profiling, they are still not routinely used in diagnostic. Microarrays, on the other hand, are more widely used for diagnostic profiling, especially for very small ncRNA (e.g., miRNAs), employing locked nucleic acid (LNA) arrays. However, LNA microarrays are quite expensive for high-throughput studies targeting longer ncRNAs, while DNA arrays do not provide satisfying results for the analysis of small RNAs. Here, we describe a mixed DNA/LNA microarray platform, where directly labeled small and longer ncRNAs are hybridized on LNA probes or custom DNA probes, respectively, enabling sensitive and specific analysis of a complex RNA population on a unique array in one single experiment. The DNA/LNA system, requiring relatively low amounts of total RNA, which complies with diagnostic references, was successfully applied to the analysis of differential ncRNA expression in mouse embryonic stem cells and adult brain cells.
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subjects Biochemistry, Molecular Biology
Biomarkers
Deoxyribonucleic acid
DNA
Genes
Genomes
Hybridization
Labeling
Life Sciences
Protocol
Stem cells
title Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray
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