title: miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes.
abstract: MicroRNAs (miRNAs) represent a class of short (22 nt) noncoding RNAs that control gene expression post-transcriptionally. Microarray technology is frequently applied to monitor miRNA expression levels but is challenged by (i) the short length of miRNAs that offers little sequence for appending detection molecules; (ii) low copy number of some miRNA; and (iii) a wide range of predicted melting temperatures (Tm) versus their DNA complementary sequences. We recently developed a microarray platform for genome-wide profiling of miRNAs (miChip) by applying locked nucleic acid (LNA)-modified capture probes. Here, we provide detailed protocols for the generation of the miChip microarray platform, the preparation and fluorescent labeling of small RNA containing total RNA, its hybridization to the immobilized LNA-modified capture probes and the post-hybridization handling of the microarray. Starting from the intact tissue sample, the entire protocol takes approximately 3 d to yield highly accurate and sensitive data about miRNA expression levels.
authors.affiliation: Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 153, Heidelberg 69120, Germany.
authors.forename: Mirco
authors.initials: M
authors.lastname: Castoldi
authors.forename: Sabine
authors.initials: S
authors.lastname: Schmidt
authors.forename: Vladimir
authors.initials: V
authors.lastname: Benes
authors.forename: Matthias W
authors.initials: MW
authors.lastname: Hentze
authors.forename: Martina U
authors.initials: MU
authors.lastname: Muckenthaler
mesh_terms: D005453:Fluorescence; D020869:Gene Expression Profiling / Q000379:methods*; D035683:MicroRNAs / Q000032:analysis*; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000378:metabolism; D009841:Oligonucleotides / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; C477371:locked nucleic acid