Agilent 2100 Bioanalyzer 2100 Expert User’s Guide s1 Notices implied, with regard to this manual and any information con- tained herein, including but not limited to the implied war- © Agilent Technologies, Inc. 2000-2006 ranties of merchantability and fitness for a particular purpose. Agilent shall not be liable for errors or for inciden- No part of this manual may be reproduced in any form or by tal or consequential damages in connection with the fur- any means (including electronic storage and retrieval or nishing, use, or performance of this document or of any translation into a foreign language) without prior agreement information contained herein. 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Further, to the maximum extent permitted by appli- cable law, Agilent disclaims all warranties, either express or Contents ▲ 2 ▼ Index Contents About this Manual ..................................................................................................................5 In this Manual............................................................................................................................. 6 Related Documents ................................................................................................................... 8 How to Use this Manual ......................................................................................................... 11 Quick Start.............................................................................................................................15 Looking at 2100 Expert .........................................................................................................29 Introduction to the Key Features of the 2100 expert.......................................................... 30 Starting 2100 Expert ................................................................................................................ 32 2100 Expert Work Area ........................................................................................................... 33 Closing 2100 Expert ................................................................................................................. 44 Running and Evaluating Electrophoretic Assays ..............................................................46 Principles of Nucleic Acid and Protein Analysis on a Chip............................................... 47 Preparing and Running an Electrophoretic Assay.............................................................. 51 Analyzing and Evaluating the Results of an Electrophoretic Assay................................ 82 Result Flagging....................................................................................................................... 157 Running and Evaluating Flow Cytometric Assays...........................................................171 Principles of Flow Cytometric Measurements.................................................................. 172 Overview of Flow Cytometric Assays ................................................................................. 181 Contents ▲ 3 ▼ Index Preparing and Running a Flow Cytometric Assay ............................................................ 184 Analyzing and Evaluating the Results of a Flow Cytometric Assay............................... 217 Working with Chip Data and Assays................................................................................264 2100 Expert Data Overview .................................................................................................. 265 Handling Assays..................................................................................................................... 268 Handling Chip Data................................................................................................................ 273 Organizing, Backing up, and Archiving 2100 Expert Data ............................................... 275 Importing Data........................................................................................................................ 277 Exporting Data ........................................................................................................................ 283 Printing Reports ..................................................................................................................... 292 Configuring Tables................................................................................................................. 299 Administering System Functions ......................................................................................305 Configuring 2100 expert........................................................................................................ 306 Using Log Books .................................................................................................................... 316 Running Instrument Diagnostics ......................................................................................322 How to Run Instrument Diagnostics Tests........................................................................ 327 Performing Verifications....................................................................................................331 Products, Spare Parts, and Accessories..........................................................................340 Glossary ...............................................................................................................................344 Contents ▲ 4 ▼ Index About this Manual Welcome to the User’s Guide for the Agilent 2100 expert software. This manual provides beginners and advanced users with information needed to successfully run electrophoretic and flow cytometric assays with the bioanalyzer. The 2100 expert software allows the control of the bioanalyzer (including diagnostic functions) and, in combination with a LabChip kit, the acquisition, interpretation and result presentation of data generated during the analysis of DNA, RNA, proteins, and cells. Contents ▲ 5 ▼ Index In this Manual This manual provides bioanalyzer users with the following information: • “About this Manual” on page 5 gives an overview of the subjects in this manual, and lists major innovations and improvements of the 2100 expert software. It also lists supplemental literature and shows you how to make efficient use of this manual. • “Quick Start” on page 15 is meant for experienced users. It briefly summarizes the necessary steps to prepare and run an assay. • “Looking at 2100 Expert” on page 29 shows how to get started with the 2100 expert software, and outlines its main operational possibilities. • “Running and Evaluating Electrophoretic Assays” on page 46 explains how electrophoretic measurements are made using the bioanalyzer, gives detailed descriptions of all steps necessary to run electrophoretic assays, and shows how to analyze and evaluate results using electropherograms and gel-like images. • “Running and Evaluating Flow Cytometric Assays” on page 171 explains how flow cytometric measurements are made using the bioanalyzer, gives detailed descriptions of all steps necessary to run flow cytometric assays, and shows how to analyze and evaluate results using histograms and dot plots. • “Working with Chip Data and Assays” on page 264 shows you what to do to open, save, import and export files, and how to print the results. • “Administering System Functions” on page 305 is your guideline for configuring the 2100 expert software. • “Running Instrument Diagnostics” on page 322 shows how to use the diagnostic tests to check the bioanalyzer hardware for proper functioning. Contents ▲ 6 ▼ Index • “Performing Verifications” on page 331 describes how you can validate your bioanalyzer system. • “Products, Spare Parts, and Accessories”