Agilent 60-mer Oligo Microarrays

Accelerating real progress with industry-first 60-mer oligo microarrays

Agilent helped fuel the early growth of microarrays by unleashing the power of arrays with the Agilent GeneArray scanner (launched as the HP GeneArray scanner in 1997) that offered enhanced resolution allowing the design of denser arrays. Over the years, Agilent capitalized on its printing know-how and ability to industrialize new technologies that came naturally from our Hewlett-Packard roots. Agilent is proud to bring all of this together to offer industry-first 60-mer oligo microarrays in a commercial, easy-to-access format.

Agilent’s 60-mer oligo microarray design emerged from in-depth studies to identify a more reliable, less redundant probe layout format than those found in 25-mer designs. By optimizing probe design algorithms, services and validation methods, Agilent can offer highly-sensitive 60-mer oligo microarrays that consistently deliver accurate results, time after time, with improved up-to-date content and coverage.

Highlights of the new 60-mer oligo microarrays

Comprehensive Coverage

A typical hybridized oligo microarray containing 22,575 features.

Highly Sensitive

Agilent’s unique 60-mer oligo format provides enhancements in sensitivity over 25-mer formats (5-8x more sensitive) partly due to the larger area available for hybridization. Agilent oligo microarrays require only one 60-mer per gene/transcript--reducing time to content updates to existing microarrays or development of new microarrays. 60-mers are also more tolerant of sequence mismatches, which results in simplified analysis of highly polymorphic regions through the use of longer probes. Former Agilent 25-mer oligo ‘custom microarray’ users have completely switched to Agilent’s highly-sensitive 60-mer probe format for all their specialized custom microarray needs a complete vote of confidence in favor of the 60-mer oligo format. (Refer to Application Note "Performance Comparison of Agilent's 60-mer and 25-mer In Situ Synthesized Oligonucleotide Microarrays" for additional information.

Control Probe Cy-3/Cy-5 Ratio gLLD (pM) rLLD (pM)
YEL009c (5:1) 0.014 0.0010
YEL009c (1:3) 0.004 0.0010
YDR345c (5:1) 0.002 0.0010
YDR345c(1:3) 0.005 0.0004
Average 0.006 0.0009
Agilent's 60-mer oligo microarray format has been shown to deliver improvements in sensitivity with the ability to detect 1 transcript/cell/million cells.

Highly Accurate

Performance control probes ensure log ratio accuracy within 1.4 fold of the expected log ratio.

Highly Reproducible

Eight Agilent 60-mer oligo microarrays yielded highly reproducible data with a median standard deviation of 0.015.

High Quality Data

Low noise leads to cleaner data and enhanced sensitivity as exemplified by the typical results of a self vs. self hybridization on a single microarray.


Highly Accessible

Oligo microarrays have become the preferred platform for studying gene expression. Researchers worldwide want access to high-quality oligo microarrays and Agilent is poised to provide a steady stream of high-content, comprehensive microarrays with better quality and performance delivered through Agilent’s 60-mer oligo format. These microarrays are fabricated with Agilent’s SurePrint technology featuring industrialized inkjet in situ oligonucleotide probe synthesis to print microarrays on-demand, with great precision-backed by extensive manufacturing QC processes.

Highly Flexible and Scalable

Agilent is the market leader in providing in an open/flexible microarray-based gene expression system build on the industry-standard 1” x 3” (25mm x 75mm) glass slide format. This provides scalability and choice for researchers. They can run Agilent microarrays on existing glass slide scanners as well as Agilent’s DNA microarray scanner. All of Agilent’s microarrays have been optimized to run on Agilent’s complete gene expression analysis system, so researchers can rest assured that they can easily add new components should the need arise.