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.

* 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 Whole Transcript Sense Target Labeling Assay Performance white paper.

  Schematic for WT Sense Target Labeling Assay.

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 and Gene Array Systems
		GeneChip® Exon Array Design
		Technical Note, Array Design for the Human Exon 1.0 ST Array (pdf, 348 KB)
		GeneChip® Exon Array Data Analysis
		White Paper, Human Gene 1.0 ST Array Performance (pdf, 620 KB)
		Technical Note, Human Gene 1.0 Array Design (pdf, 1.05 MB)