The Whole Transcript (WT) Sense Target Labeling Assay Has an Updated Protocol

The GeneChip® WT (Whole Transcript) Terminal Labeling Kit is optimized to be used for the fragmentation and labeling steps of the GeneChip® WT Sense Target (ST) Labeling Assay.

The WT Terminal Labeling Kit employs a strategy for reproducible DNA fragmentation with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1). The typical input material is random-primed, single-stranded DNA, which can be obtained using the GeneChip® WT cDNA Synthesis and Amplification Kit (available separately from Affymetrix) that incorporates deoxyuridine at predefined ratios relative to thymidine.

Following fragmentation, the resulting fragmented DNA can then be labeled using terminal deoxynucleotidyl transferase (TdT) in the presence of a proprietary biotinylated compound, GeneChip® DNA Labeling Reagent. Both components are also provided in the WT Terminal Labeling Kit. The final labeled DNA target is ready to be added to the cocktail for hybridizing to the arrays such as the GeneChip® Human Exon 1.0 ST Array.

Kit Components

Component name	For 10 Rxns	For 30 Rxns
10X cDNA Fragmentation Buffer	48 µL	144 µL
UDG, 10 U/µL	10 µL	30 µL
APE 1, 1,000 U/µL	10 µL	30 µL
5X TdT Buffer	120 µL	360 µL
TdT, 30 U/µL	20 µL	60 µL
DNA Labeling Reagent, 5 mM	10 µL	30 µL
RNase-free Water	825 µL	2x 825 µL

The GeneChip® WT Terminal Labeling Kit is also available as a component of the GeneChip® WT Sense Target Labeling and Control Reagents Kit.

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
900670	GeneChip® WT Terminal Labeling Kit	Sufficient for 10 reactions
900671	GeneChip® WT Terminal Labeling Kit	Sufficient for 30 reactions
900652	GeneChip® WT Sense Target Labeling and Control Reagents	Sufficient for 30 reactions

Related Products

Part #	Description	Details
900649	GeneChip® Human Exon 1.0 ST Array
900654	GeneChip® WT Sense Target Labeling and Control Reagents	Sufficient for 30 reactions

FAQs

Exon Array Analysis

Exon Array Design

WT Sense Target Labeling Assay

Manuals

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

Material Safety Data Sheets

WT Terminal Labeling Kit (zip, 141 KB)

Package Inserts

WT Terminal Labeling Kit (pdf, 251 KB)

Additional Support

Fluidics Scripts

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