MicroRNA expression profiling using microarrays

  title={MicroRNA expression profiling using microarrays},
  author={Chang-gong Liu and George Adrian Calin and Stefano Volinia and Carlo Maria Croce},
  journal={Nature Protocols},
Microarray technology is a powerful high-throughput tool capable of monitoring the expression of thousands of small noncoding RNAs at once within tens of samples processed in parallel in a single experiment. To conduct a genome-wide analysis of miRNA expression of normal and disease samples, such as cancer, and to distinguish expression signatures associated with diagnosis, prognosis and therapeutic interventions, we have developed a unique miRNA microarray assay on a CodeLink platform. The… 
High-throughput approaches for microRNA expression analysis.
In this chapter the high-throughput approaches that can be applied to microRNA profiling are discussed starting from small-scale qRT-PCR technology to a wider one, NGS.
Amplification-free detection of microRNAs via a rapid microarray-based sandwich assay
The optimized assay can specifically detect microRNAs in spiked samples at concentrations as low as 1 pM and from as little as 100 ng of total RNA in 2 h, correlated well with results generated by qPCR when the authors profiled a select number of breast cancer related micro RNAs in a total RNA sample.
Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines
All the platforms to be highly capable for microRNA analysis are found, including the two NGS platforms and RT-qPCR all have equally high sensitivity, and the fold change accuracy is independent of individual miRNA concentration for NGS andRT-q PCR.
Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation
The results not only demonstrated a glimpse of pre-microRNA expression in human and mouse, but also the relationship of microRNA expressions between pre- and mature forms, and showed a possible application of currently available microRNA microarrays in profiling pre- micro RNA expression in a time and cost effective manner.
Digital direct detection of microRNAs using single molecule arrays
The Simoa technique is applied to develop an ultra-sensitive sandwich assay for direct detection of multiple miRNAs without pre-amplification and was effective against a range of diverse target sequences, suggesting a general approach for miRNA detection.
Fabrication of a structure-specific RNA binder for array detection of label-free microRNA.
A novel structure specific RNA binding protein is fabricated, which stably binds to double-stranded RNAs with a 2-nt 3' overhang, which allowed us to universally detect hybridized miRNAs on array surfaces without the need of any enzymatic amplification or labeling reactions.
MicroRNA Expression Analysis: Next-Generation Sequencing.
A detailed procedure of generation of miRNA library for next-generation sequencing to increase the efficiency of adapter ligation and finally construct a more specific cDNA library for sequencing and analyses for miRNA expression profiling is described.
Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications
This fast and reliable methodology allowed us to identify mutations in tumors with remarkable sensitivity and to perform integrative analyses of whole-genome and exome data sets, DNA copy numbers, gene expression data, and protein levels from the same samples.
MicroRNA Profiling and Its Application in Drug Discovery in Pancreatic Cancer
This chapter discusses the various profiling methods applied to the identification of differentially expressed miRNAs in Pancreatic cancer, which can applied towards drug development for pancreatic cancer.
A multiplex sensitive quantification of microRNAs based on competitive PCR
This method enables multiplex, accurate and sensitive quantification of miRNAs with fewer precious RNA samples than qRT-PCR, and compares the expression level of miR-505-3p in two tissues between C57BL/6J and C3H/HeJ mice.


A high-throughput method to monitor the expression of microRNA precursors.
A sensitive, high throughput, real-time PCR assay to monitor the expression of miRNA precursors and proposes that the PCR assay may be scaled up to include all of the 150+ known human miRNA genes and can easily be adaptable to other organisms such as plants, Caenorhabditis elegans and Drosophila.
A custom microarray platform for analysis of microRNA gene expression
Dual-channel microarrays are designed that monitor expression levels of 124 mammalian microRNAs and expression profiles of staged embryos demonstrate temporal regulation of a large class of micro RNAs, including members of the let-7 family.
An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues.
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 is described.
Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.
A simple, robust, inexpensive assay for quantitative analysis of microRNAs and short-interfering RNAs based on primer extension conversion of RNA to cDNA by reverse transcription followed by quantitative, real-time PCR.
Real-time quantification of microRNAs by stem–loop RT–PCR
A novel microRNA quantification method has been developed using stem–loop RT followed by TaqMan PCR analysis, which enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases.
MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias.
Genomewide expression profiling of miRNAs in human B cell chronic lymphocytic leukemia (CLL) is reported by using a microarray containing hundreds of human precursor and mature miRNA oligonucleotide probes, suggesting that miRNA expression patterns have relevance to the biological and clinical behavior of this leukemia.
MicroRNA gene expression deregulation in human breast cancer.
It is shown that, compared with normal breast tissue, miRNAs are also aberrantly expressed in human breast cancer, and the overall miRNA expression could clearly separate normal versus cancer tissues, with the most significantly deregulated mi RNAs being mir-125b, mir-145, mir -21, and mir-155.
MicroRNA expression profiles classify human cancers
A new, bead-based flow cytometric miRNA expression profiling method is used to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers, and finds the miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours.
The colorectal microRNAome.
It is suggested that the human genome contains many more miRNAs than currently identified and an experimental approach called miRNA serial analysis of gene expression (miRAGE) is developed and used to perform the largest experimental analysis of human mi RNAs to date.
A microRNA expression signature of human solid tumors defines cancer gene targets
  • S. Volinia, G. Calin, C. Croce
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2006
The results indicate that miRNAs are extensively involved in cancer pathogenesis of solid tumors and support their function as either dominant or recessive cancer genes.