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eArray - Details & Specifications

Custom Microarray Steps

Agilent supports a variety of formats, probes, genomic applications, and species. To design a microarray, you need to determine the right combination of options that meets your specific experimental needs.

The typical planning process includes:

  1. Choose an RNA or DNA application that generates the appropriate data for your experimental needs
    Your experimental plan will dictate the genomic technique to use or measurement to make. Agilent has optimized and supports several RNA and DNA applications for transcript RNA and/or genomic DNA, including Gene Expression, array-based CGH (comparative genomic hybridization), and array-based ChIP (chromatin immunoprecipitation). In addition to these standard techniques, we have also printed microarrays for customers studying miRNA, siRNA, alternative splicing, methylation, and more. Agilent can generally print anything you need, even if we do not provide a processing protocol or an end-to-end processing solution.

  2. Specify the organism you are representing
    Agilent has an extensive library of pre-designed probes for a number of species. This library can be searched and the resulting probes re-purposed according to your custom needs. From a probe design perspective, specifying eukaryotic versus prokaryotic organisms allows us to optimize probe design according to the differing genome base composition of these biological groups.

  3. Design probes against your target sequence database or select from our library and submit to Agilent
    You can use Agilent probes, your own probes, or a combination of both to design your custom microarray. If you are designing your own, we will provide design guidelines and data formats that are compatible with our systems. While our standard probe length is a 60-mer, we will print any length between 25 and 60 bases. For variable length probe sets, we can design tethers to generate uniform 60-mers or print variable length probes. The process includes:


    • Sequence curation
    • Vector masking
    • Repeat masking
    • Probe selection

  5. Choose an array format to accommodate the number of probes you wish to print
    Agilent offers a variety of microarray formats to choose from according to your application and content requirements. All of our microarrays are built on industry-standard 1 x 3 inch glass slides.


8 x 15k
4 x 44k
2 x 105k
1 x 244k
  SurePrint G3
8 x 60k
4 x 180k
2 x 400k
1 x 1m


Design the microarray yourself using eArray or engage our team's Professional Consulting Services

Customers have two options for generating their designs with Agilent. The most efficient and economical path is via eArray, our web design application that puts the power of our design and manufacturing capabilities in your hands. For conventional applications and experienced genomics data managers, eArray is a powerful tool that puts you in control of project management. For boutique applications or less experienced customers, Agilent continues to offer a comprehensive consulting service for probe design, annotation, genome assembly, and more.

Array Layout - an aspect of the collaborative design service that gives you complete flexibility in your design. The processes enables you to rapidly iterate and print new array layouts. Within your custom microarray design, you can:


  • Use customer-designed probes between 25-60 bases long
  • Use Agilent-designed 60-mer probes
  • Randomize probe placement on the microarray
  • Define probe placement on the microarray
  • Layout formats between ~11k and ~44k spots per slide.


Basic QC - analysis of the design quality includes:


  • Probe sequence curation
  • Probe base composition and melting temperature evaluation (Tm)


Professional Consulting Services enables you to provide generic requirements in the creation of your array design. Whether you’re just considering microarray solutions or currently running microarrays, you may require some consultation to help figure out what microarray solution is right for you, or even how to streamline your current microarray testing format. Services could include:


  • EST clustering and Assembly
  • Target Search and Retrieval
  • Domain Target Identification
  • Array Annotation
  • Specialty Arrays 


Order microarrays through eArray or through your local Agilent sales representative

Custom microarrays and related designs services cannot be purchased through standard Agilent e-channels because of the nature of pricing customer specifications. For pricing information, contact your Agilent local sales representative. Once designs are complete and a valid order is opened, microarray deliveries can be requested using either eArray or by contacting you sales rep. In either case, your microarrays will be delivered in weeks, not months.

Agilent custom microarrays offer customers maximum content flexibility, state-of-the-art manufacturing and quality control, and project management value that is unsurpassed in the industry. Call us today to discuss your specific project needs and we'll get you started down the path to scientific success.

For Research Use Only. Not for use in diagnostic procedures