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4 GeneChipTM Expression Analysis Technical Manual
Overnight Hybridization ...................................................................................................................................... 75
Section 3: Wash & Stain ........................................................................................................... 76
Introduction ......................................................................................................................................................... 76
Reagents and Materials for Wash and Stain ........................................................................................................ 76
Wash and Stain Preparation ....................................................................................................... 77
Stain Dispensing Setup Protocol ......................................................................................................................... 78
Clean the Bio-Rad Plate Lids with DNAZap™ and RNaseZapTM ........................................................................ 80
Manual Stain Dispensing Setup........................................................................................................................... 85
Clean the Bio-Rad Plate Lids with DNAZap™ and RNaseZapTM ...................................................................... 85
Automated Wash and Stain Protocol .......................................................................................... 86
Automated Wash and Stain Schematic ................................................................................................................ 86
Beginning a Run – Wash and Stain Deck Layout ............................................................................................... 88
Reagent Setup for Wash and Stain Protocol ........................................................................................................ 90
Running the Wash and Stain Protocol......................................................................................... 91
Running the Protocol ........................................................................................................................................... 91
Chapter 6 Hybridization, Wash and Stain Protocol with User-
prepared Reagents ............................................................ 96
Introduction ............................................................................................................................ 96
Reagents and Materials Master List for Hybridization, Wash and Stain .......................................... 96
Section 1: Hybridization Setup .................................................................................................. 98
Introduction ......................................................................................................................................................... 98
Reagents and Materials for Hybridization Setup ................................................................................................. 98
Reagent Preparation ............................................................................................................................................ 99
Automated Hybridization Setup Schematic ........................................................................................................ 99
Pre-Hybridization Buffer for HT Array Plates .................................................................................................... 99
Beginning a Run – Deck Layout for Hybridization Setup ............................................................ 101
Procedure - Assembling the Deck ..................................................................................................................... 101
Running the Hybridization Setup Protocol ................................................................................ 103
Section 2: Hybridization ......................................................................................................... 111
Overnight Hybridization .................................................................................................................................... 111
Section 3: Wash & Stain ......................................................................................................... 112
Introduction ....................................................................................................................................................... 112
Reagents and Materials for Wash and Stain ...................................................................................................... 112
Wash and Stain Preparation .................................................................................................... 113
Reagent Preparation .......................................................................................................................................... 113
Stain Dispensing ................................................................................................................................................ 116