Anyone have any working ideas for microarrays for miRNA ? Affymetrix says their exon chip cannot be used. What are the others using right now ?

Fizz:

Here are some online resources that may be of help.


Invitrogen NCode miRNA Analysis

NCode miRNA Microarray and Probe Set Information

The NCode Multi-Species miRNA Microarray V2 contains probes that target all of the miRNA species in Sanger mirBase 9.0 for human, mouse, rat, Drosophila, C. elegans, and zebrafish (Figure 1). The arrays are spotted in triplicate, contain controls for monitoring hybridization specificity, include dye normalization controls, and have positive and negative controls spotted throughout the array.



Ambion mirVana miRNA Probe Set

Ambion mirVana miRNA Bioarrays Version 2 (Cat #1566V2) Instruction Manual

The mirVana miRNA Probe Set (patent pending) is a collection of amine-modified DNA oligonucleotides targeting a comprehensive selection of human, mouse, and rat miRNAs from miRBase Sequence Database version 8.0. In addition, the mirVana miRNA Probe Set includes probes targeting an exclusive set of newly identified human miRNAs. Called Ambi-miR miRNAs, these novel miRNAs were identified through a combination of bioinformatic prediction, cloning, and detection in human total RNA samples. Developed in conjunction with the mirVana miRNA Labeling Kit, the mirVana miRNA Probe Set is designed for preparation of glass slide miRNA arrays". Using the mirVana Array System (see Figure 2), you can analyze global miRNA expression profiles using commercially available microarray analysis instruments and software.

The probes in the mirVana miRNA Probe Set are 4246 nucleotides (nt) long and consist of an 1824 nt segment that targets a specific known human, mouse, or rat miRNA, plus spacer and attachment sequences for coupling to the surface of the microarray slide. The probes are synthesized with an amine-modification for compatibility with both epoxy and aldehyde slide surface attachment chemistries. We recommend SCHOTT Nexterion Slide E microarray slides as they are convenient, easy to use, and provide consistent results. However, the mirVana miRNA Probe Set is compatible with all common array attachment chemistries except 3-D gel matrix slides. (Gel matrix slides are incompatible with the spacer and linker sequences within the miRNA Probe Set oligonucleotides.)

Note: Overview of this Ambion product was cited from the linked product page



Agilent Technologies Human miRNA Microarray Kit

The Human miRNA Microarray contains probes for 470 human and 64 viral microRNAs from the Sanger database v9.1. Integrating Agilent's probe design and unique labeling methods, this microarray delivers robust data with a simple, streamlined protocol. The generation of complete miRNA expression profiles using robust and highly sensitive microarrays allows broad insight into human miRNA expression and regulation.

Note: Overview of this Agilent product was cited from the linked product page




Here are some publications you may be interested in concerning miRNA microarrays:


Eric A Miska, Ezequiel Alvarez-Saavedra, Matthew Townsend, Akira Yoshii, Nenad estan, Pasko Rakic, Martha Constantine-Paton, and H Robert Horvitz. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biology 2004, 5:R68.

Background
MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates microRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death and fat metabolism. Little is known about the roles of microRNAs in mammals.

Results
We isolated 18-26 nucleotide RNAs from developing rat and monkey brains. From the sequences of these RNAs and the sequences of the rat and human genomes we determined which of these small RNAs are likely to have derived from stem-loop precursors typical of microRNAs. Next, we developed a microarray technology suitable for detecting microRNAs and printed a microRNA microarray representing 138 mammalian microRNAs corresponding to the sequences of the microRNAs we cloned as well as to other known microRNAs. We used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain.

Conclusion
We describe a microarray technology that can be used to analyze the expression of microRNAs and of other small RNAs. MicroRNA microarrays offer a new tool that should facilitate studies of the biological roles of microRNAs. We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs.



Ru-Qiang Liang, Wei Li, Yang Li, Cui-yan Tan, Jian-Xun Li, You-Xin Jin, and Kang-Cheng Ruan. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 2005; 33(2): e17.

Abstract
MicroRNAs (miRNAs) play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. They have diverse expression patterns and might regulate various developmental and physiological processes. Profiling miRNA expression is very helpful for studying biological functions of miRNAs. We report a novel miRNA profiling microarray, in which miRNAs were directly labeled at the 3′ terminus with biotin and hybridized with complementary oligo-DNA probes immobilized on glass slides, and subsequently detected by measuring fluorescence of quantum dots labeled with streptavidin bound to miRNAs through streptavidinbiotin interaction. The detection limit of this microarray for miRNA was ∼0.4 fmol, and the detection dynamic range spanned about 2 orders of magnitude. We made a model microarray to profile 11 miRNAs from leaf and root of rice (Oryza sativa L. ssp. indica) seedlings. The analysis results of the miRNAs had a good reproducibility and were consistent with the northern blot result. To avoid using high-cost detection equipment, colorimetric detection, a method based on nanogold probe coupled with silver enhancement, was also successfully introduced into miRNA profiling microarray detection.



Chang-Gong Liu, George Adrian Calin, Brian Meloon, Nir Gamliel, Cinzia Sevignani, Manuela Ferracin, Calin Dan Dumitru, Masayoshi Shimizu, Simona Zupo, Mariella Dono, Hansjuerg Alder, Florencia Bullrich, Massimo Negrini, and Carlo M. Croce. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. PNAS. June 29, 2004 Vol. 101, No. 26

Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNA genes recently found to be abnormally expressed in several types of cancer. Here, we describe a recently developed methodology for miRNA gene expression profiling based on the development of a microchip containing oligonucleotides corresponding to 245 miRNAs from human and mouse genomes. We used these microarrays to obtain highly reproducible results that revealed tissue-specific miRNA expression signatures, data that were confirmed by assessment of expression by Northern blots, real-time RT-PCR, and literature search. The microchip oligolibrary can be expanded to include an increasing number of miRNAs discovered in various species and is useful for the analysis of normal and disease states.

Arecently discovered class of small noncoding RNAs, named microRNAs (miRNAs), has been identified in plants and animals. The 19- to 22-nt active product is processed from a 60- to 110-nt pre-miRNA hairpin transcript thought to derive from a longer pre-miRNA product. It is believed that miRNAs act to regulate gene expression during development and differentiation, at the transcriptional and/or translational level, although targets are still elusive. We have previously shown frequent deletions and down-regulation of miR-15a and miR-16-1 miRNAs genes at 13q14 in B-cell chronic lymphocytic leukemia, the most common adult leukemia in the Western world. We also reported that human miRNA genes are frequently located at fragile sites and genomic regions involved in cancers, suggesting that the role of miRNA in human cancer may involve more than a few genes. In fact, two recent papers reported reduced accumulation of miR-145 and miR-143 in colorectal neoplasia and high expression of precursor miRNA-155/BIC RNA in children with Burkitt's lymphoma. Assessing cancer-specific expression levels for hundreds of miRNA genes is time consuming, and requires a large amount of total RNA (at least 20 g for each Northern blot) and autoradiographic techniques that require radioactive isotopes. To overcome these limitations and investigate alterations in expression of all known miRNAs in human cancer, we developed a miRNA microarray and established detection methodology for miRNA expression that overcomes the size limitation imposed by their length (18-22 nt).

Thanks for the detailed reply Tony. That helps :)
Just a heads up again. Affymetrix does NOT recommend using their exon array for miRNA probing.