Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI cancer cells. We have conducted a study to compare the variability in measured gene expression levels associated with three types of microarray platforms. Total RNA. DNA oligonucleotides are spotted onto the array. The main feature of oligonucleotide microarrays is that each gene is normally represented by more than one.


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Oligonucleotide Array Sequence Analysis - MeSH Result

Arrays from commercial vendors may have as few as 10 probes or as many as 5 million or more micrometre-scale probes. The probes are synthesized prior to deposition on the array surface and are then "spotted" onto glass.

A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations oligonucleotide array the array surface.

The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or oligonucleotide array "targets" derived from experimental or oligonucleotide array samples.

This technique is used by research scientists around the world to produce "in-house" printed microarrays from their own labs.

A Comparison of cDNA, Oligonucleotide, and Affymetrix GeneChip Gene Expression Microarray Platforms

These arrays may be easily oligonucleotide array for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab or collaborating facility oligonucleotide array, and spot the arrays.

They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment.

This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often oligonucleotide array expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator.

Publications exist oligonucleotide array indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays, [15] possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays.

In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading oligonucleotide array.

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Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. The difference is that these chips contain the oligos, and not the targets.

The length oligonucleotide array the oligos oligonucleotide array depends on the oligonucleotide array, but they are usually no longer than 25 bases. Since oligos are usually shorter, the density is much higher in these chips. GeneChip system with an oligonucleotide representation of tens of thousands genes, covering an entire genome; different genomes are currently available human, mouse, Drosophila and others.

Oligonucleotide microarrays

For technical reasons, only oligonucleotide array single sample can be measured on one of these chips; thus experiments using oligonucleotides microrarrays are often referred as single channel hybridization. Thus success depends on tightly controlled array production and hybridization methods.

The amount of variation within a technology and the amount of agreement across the oligonucleotide array platforms are important issues for researchers and core laboratories.


A number of studies have been conducted to compare different platforms but there is no clear consensus. Initially, cDNA libraries were predominant, but because of concerns about annotation, clone identity, and probe performance, 8 long oligonucleotide 50—70 oligonucleotide array platforms have become increasingly popular.

Commercially available oligonucleotide libraries have gained acceptance in recent years because the annotation and identity of oligonucleotides in these libraries are oligonucleotide array and the hybridization characteristics of oligonucleotides are generally good.