Agilent Microarray Technology

Agilent is advancing the art of manufacturing microarrays with SurePrint, a powerful combination of probe design algorithms and validation methods, maskless & highly-flexible microarray printing based on industrial-scale inkjet technologies, and unique QC processes.

The result is affordable, accessible pre-printed microarrays that content researchers can trust. Find out more about the powerful SurePrint, SureScan, and SureHyb technologies behind Agilent's microarray platform!


SurePrint Technology


Agilent 1,000,000-feature microarrays represent a four-fold increase in density compared with our previous microarray series. The dramatic increase in genomic coverage lets researchers use the superior performance of Agilent arrays in a growing number of high-resolution genomic applications.

SurePrint technology allows as many as 8 arrays to reside on a single slide, allowing experiments to range from a genome-wide view to more focused studies. Researchers can now design ever-larger, more powerful microarray experiments very cost effectively.

While Agilent offers a wide range of catalog microarrays, they can also be easily customized to enable the widest possible range of experimentation. Using eArray, an easy-to-use web-based application, researchers can rapidly design custom microarrays in a secure online environment at no additional cost. Agilent supports a variety of formats, probes, genomic applications, and species, from which researchers can determine the right combination of options to meet specific experimental needs. Once a custom design has been completed, Agilent SurePrint inkjet technology ensures rapid manufacturing, with delivery in three to six weeks, depending on geography.

In Situ Synthesis Printing Process

Both catalog and custom microarrays are manufactured using a proprietary non-contact industrial inkjet printing process, in which oligo monomers are deposited uniformly onto specially-prepared glass slides. This in situ synthesis process prints 60-mer length oligonucleotide probes, base-by-base, from digital sequence files. The precise inkjet process enables the delivery of extremely small, accurate volumes (picoliters) of the chemicals to be spotted. Figure 1 highlights four steps in the process, and a short animation shows the process in action.

View animation video (8MB, 36sec)

Standard phosphoramidite chemistry used in the reactions allows for very high coupling efficiencies to be maintained at each step in the synthesis of the full-length oligonucleotide (Figure 2). Precise quantities are reproducibly deposited “on the fly.” This engineering feat is achieved without stopping, to make contact with the slide surface and without introducing surface-contact feature anomalies, resulting in consistent spot uniformity and traceability. In addition, multiple microarrays can be printed simultaneously in a single manufacturing run.



Figure 1. These four images communicate the general mechanism for oligo synthesis via inkjet printing. A: the first layer of nucleotides is deposited on the activated microarray surface. B: growth of the oligos is shown after multiple layers of nucleotides have been precisely printed. C: close-up of one oligo as a new base is being added to the chain, which is shown in figure D.



Figure 2. The general cycle of oligo synthesis via phosphoramidite chemistry. The process is repeated 60 times.

Real Time Quality Control

Agilent’s real time quality control inspection system verifies chemical deposition at each step in the process to minimize or eliminate feature drop-out and premature truncation of the oligonucleotide probe. With Agilent's unique in situ process, oligonucleotides of 60 bases in length can be synthesized to create high-quality, fast-turnaround custom microarrays.



SureScan Technology

Agilent's performance-leading microarray scanner just got better

Agilent has been in the microarray scanning business for over a decade. In 1997, Agilent unleashed the power of Affymetrix technology with the Agilent, then HP, GeneArray scanner. In 2001, Agilent launched it's next generation scanner that provided enhanced sensitivity for Agilent's microarray platform, and followed this release with improved performance for non-Agilent slides in 2002. Now as Agilent prepares for its next wave of high-density microarrays, the microarray scanner has evolved to meet the challenge with the introduction of high-resolution scanning capability.

 

Key Technologies

 

High-Resolution scanning

5µm 2µm  
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The image on the left shows a region of a 30 micron feature array scanned at 5 micron resolution. The image on the right shows the same region of the array scanned at 2 micron resolution on the new high-resolution Agilent scanner. Note the improvement in the image quality.

 

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As illustrated by the diagram above, the number of pixels useable for image analysis decreases dramatically as the feature size decreases. Increasing the scan resolution regains the number of pixels available for analysis.



Industry-first Dynamic Autofocus

 

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Even the most revered glass manufacturer can't manufacture a glass slide without some warpage, curvature or changes in glass thickness. All of these glass variations can cause problems with microarray scanner laser focus calibration. Many manufacturers have incorporated a single focus laser calibration, but this only occurs on one part of a glass slide and doesn't compensate for potential variability across the slide.

Agilent has engineered a better approach to remove this variable in microarray analysis. Agilent's Dynamic Autofocus feature delivers increased sensitivity by continuously adjusting the focal plane, correcting for common glass surface abnormalities and gradients as well as any potential slide movement within the scanner. Incredibly, this Dynamic Autofocus feature is able to adjust over 1 million times during the course of a microarray scan and helps keep every feature/spot in focus.



Extended Dynamic Range (XDR) and 20 bit scanning

Extended Dynamic Range (XDR)  
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For many applications, including gene expression and miRNA, the sample's dynamic range exceeds the 16-bit range that traditional scanners have offered. This forces users to make decision between a high-sensitivity setting in which many features on the array will saturate, and a low-sensitivity setting in which few or no features saturate but the ability to detect weak probes is limited. In 2006, Agilent solved this dilemma with the introduction of extended dynamic range (XDR). In XDR mode, the scanner performs a dual scan, the first at the most sensitive PMT setting, and the second at a lower PMT setting. Agilent's Feature Extraction software then combines the data in a robust manner by checking the data in the overlap region for consistency and reporting any discrepancy that may occur. As a result, users can realize a 10-20 fold increase in dynamic range which more closely matches the dynamic range of the microarray and the biological sample.
20 bit scanning  
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With the introduction of the high-resolution scanner, Agilent is has improved upon XDR scanning by increasing the dynamic range of a single scan from 16-bit to 20-bit thereby realizing the same dynamic range as with XDR scanning but with a single scan. Now instead of saturating at 65,535 counts as with a 16-bit scan, the new saturation value is 12 times larger at over 780,000.

For Research Use Only. Not for use in diagnostic procedures