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GeneChip® Expression Analysis Technical Manual

Description of Update

This update to the GeneChip® Expression Analysis Technical contains several important changes and replaces all previous GeneChip Expression assay protocols. Please feel free to discard or archive all previous GeneChip expression assay protocols.

This update includes the following changes and new information:

  • Target preparation and fluidics script protocols are now also provided for the new 169 Format prokaryotic arrays, such as the GeneChip E.coli Genome 2.0 Array.

  • Updated Eukaryotic Target Labeling Assays are described in Section 2, Chapter 1. The new protocols include detailed instructions for using new GeneChip® Reagents (including the Poly-A RNA Control Kit, the One-Cycle cDNA Synthesis Kit, the Two-Cycle cDNA Synthesis Kit, and the IVT Labeling Kit), in both the One-Cycle and two-Cycle Target Labeling Assays, with robust performance for 1-15 µg and 10-100 ng of total RNA as starting material respectively.

  • Associated with the new protocols, optimized hybridization and wash conditions were developed to provide superior performance on the higher density, 11µm feature size GeneChip® arrays. Detailed information on the new hybridization and wash procedures is described in Section 2, Chapter 2 and 3.

  • Frequently Asked Questions and Troubleshooting is updated to support the new assays and reagents in Appendix B.

  • The previously recommended "Standard Target Labeling Assay" has been replaced by the new One-Cycle target Labeling Assay, and now is found within section 2 as an “alternative protocol.”

  • Updated Prokaryotic Target Labeling Assay is described in Section 3, Chapter 1. This new assay replaces the previous recommendation and utilizes a new GeneChip® DNA Labeling Reagent for terminal labeling of the fragmented cDNA target. Instruction for using the Poly-A RNA Control kit for the prokaryotic assay is also included in this chapter.

  • For instrument control of the GeneChip® Fluidics Station and GeneChip® Scanner 3000, the steps using the GeneChip® Operating System were also outlined in addition to the previous-generation Microarray Suite software.