Complementary to the Exon and Gene Array Design for Optimal Sensitivity and Specificity

Complete reagent solution for confidence and convenience

As a critical part of the integrated system, complete reagent kits have been developed, validated, and qualified specifically for the GeneChip® Exon and Gene 1.0 ST Arrays. These reagent kits provide convenience as well as high-quality results and consistent data.

Generating sense DNA targets along the entire length of the transcript

Using a random priming strategy, in combination with in vitro transcription-based linear amplification and a novel end-point fragmentation and labeling assay scheme, the Whole Transcript (WT) Sense Target Labeling Assay provides a robust method for target labeling. The key differences for the two configurations of the WT Assay are indicated in the table below.

	1µg Total RNA Labeling Protocol	100 ng Total RNA Labeling Protocol
Recommend Amount of Starting Material	1 µg Total RNA	100 ng Total RNA
Acceptable Range of Input Amount	1-2 µg*	100-300 ng
Procedural Difference	Requires rRNA Reduction with RiboMinus Kit	Omits rRNA Reduction
Exon ST Arrays	Recommended	Not Optimal
Gene ST Arrays	Acceptable	Recommended

* When using 2 µg of starting material, it is highly recommended to scale up the RiboMinus reagents to ensure efficient rRNA reduction. Failure to do so may have a small negative impact on sensitivity, particularly at the exon level.

One µg or 100 ng of total RNA is recommended as starting material following the assay described in the schematic shown below. The 100 ng of total RNA protocol bypasses the initial ribosomal RNA (rRNA) reduction step. The rRNA reduction becomes critical when a user is interested in high-sensitivity analysis of expression levels for both genes and exons using the GeneChip® Exon 1.0 ST Arrays. This is because exon probe sets contain a smaller number of probes and, in some cases, selection of those probes is constrained by the limited size of the probe selection region. Therefore, it is imperative to use the high-sensitivity assay for optimal performance.

On the other hand, analysis of the gene level benefits from a larger number of high-quality probes selected from the entire transcript, thus the advantage of the additional rRNA reduction step is reduced. Hence, the 100 ng Total RNA Labeling Protocol is acceptable for use with GeneChip® Gene 1.0 ST Arrays. For more information regarding the performances of the two protocols on Gene 1.0 ST Arrays, refer to the White paper (pdf, 801 KB) for the Whole Transcript Sense Target Labeling Assay performance.

Kit Component *	Quantity
GeneChip® WT cDNA Synthesis and Amplification Kit	1
GeneChip® WT Terminal Labeling Kit	1
GeneChip® Sample Cleanup Module	1
GeneChip® IVT cRNA Cleanup Kit	1**
GeneChip® Eukaryotic Poly-A RNA Control Kit	1
GeneChip® Hybridization Control Kit	1

*Required reagents which are not included in the kit: RiboMinus™ Human/Mouse Transcriptome Isolation Kit from Invitrogen.
**Not required in specific bundle kits.

Read More

• GeneChip® Exon Array Design
• Technical Note, Array Design for the Human Exon 1.0 ST Array (pdf, 348 KB)
• White Paper, Human Gene 1.0 ST Array Performance (pdf, 620 KB)

Data Sheets

Exon Array System (pdf, 464 KB)

Technical Notes

Array Design for the Human Exon 1.0 ST Array (pdf, 348 KB)

Human Exon 1.0 ST Array and WT Sense Target Labeling Assay for Genome-Wide, Exon-Level Expression Analysis (pdf, 624 KB)

Application Notes

Whole-transcript Expression Analysis (pdf, 557 kb)

Part #	Description	Details
900652	GeneChip® WT Sense Target Labeling and Control Reagents	Sufficient for 30 reactions
900654	GeneChip® Human Exon 1.0 ST Array Starter Pack	Contains 30 arrays and 30 reactions of reagents
900831	GeneChip® Mouse Exon 1.0 ST Array Starter Pack	Contains 30 arrays and reagents sufficient for 30 reactions
900848	GeneChip® Rat Exon 1.0 ST Array Starter Pack	Contains 30 arrays and reagents sufficient for 30 reactions
901147	GeneChip® Human Gene 1.0 ST Arrays and Reagents, 10 Pack	Contains 10 arrays and reagents sufficient for 10 reactions
901146	GeneChip® Human Gene 1.0 ST Arrays and Reagents, 30 Pack	Contains 30 arrays and reagents sufficient for 30 reactions

Related Products

Part #	Description	Details
900649	GeneChip® Human Exon 1.0 ST Array
900817	GeneChip® Mouse Exon 1.0 ST Array
900820	GeneChip® Rat Exon 1.0 ST Array
901085	GeneChip® Human Gene 1.0 ST Array
901168	GeneChip® Mouse Gene 1.0 ST Array
901172	GeneChip® Rat Gene 1.0 ST Array
900720	GeneChip® Hybridization, Wash, and Stain Kit
00-0211	GeneChip® Scanner 3000 7G with Workstation
00-0079	GeneChip® Fluidics Station 450

FAQs

Exon Array Analysis

Exon Array Design

WT Sense Target Labeling Assay

Manuals

Whole Transcript (WT) Sense Target Labeling Assay (pdf, 1.12 MB)

Package Inserts

Eukaryotic Poly-A RNA Control Kit (pdf, 36 KB)

Hybridization Control Kit (pdf, 59 KB)

IVT cRNA Cleanup Kit (pdf, 270 KB)

Sample Cleanup Module (pdf, 55 KB)

WT cDNA Synthesis and Amplification Kit (pdf, 253 KB)

WT Terminal Labeling Kit (pdf, 251 KB)

Additional Support

Fluidics Scripts

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