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Genomic and RNA Profiling Core Facility

Houston, Texas

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Genomic and RNA Profiling Core
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Agilent Expression Arrays

Agilent printing Image provided courtesy of Agilent Technologies

Agilent’s proprietary SurePrint technology uses an inkjet, non-contact printing process to produce glass arrays containing 60-mer oligonucleotide probes. Since this in situ process prints from digital sequence files, it allows for efficient printing of both catalog arrays and custom arrays. Up to eight arrays can be printed on one slide, giving researchers the ability to view either entire genomes or a smaller pool of genes.


mRNA Expression

Agilent's Dual-Mode Gene Expression Analysis Platform delivers both the ease of one-color experimental design and the resolving power of two-color detection in one platform. Agilent has developed a gene expression system that utilizes 60-mer oligonucleotide microarrays for either one-color (single sample Cy3) or two-color (Cy3 and Cy5) analysis. Please visit the Agilent website for array formats and organism types.

Agilent RNA Expression Assays
Labeling Technology Minimum Total RNA Input Minimum Concentration
1-Color

50 ng (Total RNA) - 4x and 8x arrays

200 ng (Total RNA) - 1x and 2x arrays

10 ng (polyA RNA)

34 ng/uL (Total RNA) - 4x and 8x arrays

134 ng/uL (Total RNA) - 1x and 2x arrays

1.9 ng/µL (polyA RNA)

2-Color

50 ng (Total RNA)

10 ng (polyA RNA)

6 ng/µL (Total RNA)

1.2 ng/µL (polyA RNA)


microRNA Expression

Agilent miRNA array platform combines the miRNA direct labeling method with an innovative probe design that allows researchers to study expression and regulation while requiring low amounts of input RNA. Because miRNAs are potential regulators of gene expression, scientists are increasingly interested in measuring them for research, drug discovery, and eventually diagnostic tests. This assay provides rapid design and validation of probes while quantitatively measuring miRNA sequences. Please visit the Agilent website for array formats and organism types.

Agilent microRNA Expression Assay
Total RNA Input Minimum Concentration Total RNA Concentration
100 ng 6 - 10% 50 ng/µL (Total RNA)

NuGEN for Agilent

Amplified RNA samples from these systems are subsequently hybridized to Agilent expression arrays overnight. Please reference the chart below to determine NuGEN system and Affymetrix array compatibility. For more information about NuGEN Product, please click here.

NuGEN FFPE Workflow

Agilent Expression Alternative Labeling - NuGEN Technologies, Inc.

NuGEN Kit Minimum Total RNA Input Minimum Total RNA Concentration
Ovation RNA Amplification System V2 50 ng 25 ng/µL
Ovation Pico WTA System V2 500 pg 100 pg/µL
Ovation FFPE WTA System

10 ng (intact RNA)

50 ng (degraded RNA)

2 ng/µL (intact)

10 ng/µL (degraded)

For users wanting to submit FFPE samples, GARP recommends using NuGEN's Prelude FFPE RNA Isolation kit, which is included with the Ovation FFPE WTA System, or an isolation kit specially designed for FFPE tissues extractions manufactured by Qiagen or Zymo. For customers wanting to submit FFPE samples for microarray analysis using NuGEN's Ovation FFPE WTA System, please contact GARP to request the kit order and submit billing information. Please include a note that you will want to use the Prelude FFPE RNA Isolation kit enclosed with WTA kit. Since GARP does not perform RNA or DNA isolations, users will need to pick up the Prelude kit and perform these isolations prior to submitting RNA samples for SAQC. Users will be billed for the entire Ovation FFPE WTA kit, no partial billing.


Please visit the Agilent website for array formats and organism types. Also see NuGEN's Agilent Solution Application Note for details.

NOTE: All samples must pass GARP Sample Quality Control SAQC before they can be submitted for array processing. Please click here for sample specifications for Affymetrix and Agilent arrays.

NuGEN for Affymetrix

NuGEN has revolutionized amplification and labeling technologies that enable life science researchers to mine genomic samples from extremely small, degraded, and hard-to-replace specimens. The Ovation® RNA Amplification System V2 uses as little as 5 ng of total RNA (although at least 20 ng is recommended). This amplification system is 3’ bias, but only one round of amplification is performed which covers ~1500 bases from the poly A tail.

For samples with even stricter concentration restraints, the Ovation™ Pico WTA System V2 requires only 500 pg of total RNA and a single round of amplification. This system incorporates oligo dT and random primers for amplification at the 3’ end and throughout the whole transcriptome. Consequently, partially degraded RNA samples prepared using the WT-Ovation™ Pico System provide adequate amplified product.

For severely degraded samples, such as FFPE tissue derived RNA samples, NuGEN provides the Ovation™ FFPE WTA System. This system also amplifies throughout the entire transcriptome in addition to the 3’ end. Intact total RNA has been tested on this system with successful results, requiring only small amount of sample input.

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