Agilent Technologies 2100 Bioanalyzer System User manual

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Agilent 2100 Bioanalyzer
2100 Expert User’s Guide

Contents ▲2▼Index
Notices
© Agilent Technologies, Inc. 2000-2005
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Manual Part number: G2946-90004
Edition: May 2005
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Contents ▲3▼Index
Contents
About this Manual ..................................................................................................................5
In this Manual............................................................................................................................. 6
Related Documents ................................................................................................................... 8
How to Use this Manual ......................................................................................................... 10
Quick Start.............................................................................................................................14
Looking at 2100 Expert .........................................................................................................28
Introduction to the Key Features of the 2100 expert.......................................................... 29
Starting 2100 Expert ................................................................................................................ 31
2100 Expert Work Area ........................................................................................................... 32
Closing 2100 Expert ................................................................................................................. 43
Running and Evaluating Electrophoretic Assays ..............................................................45
Principles of Nucleic Acid and Protein Analysis on a Chip............................................... 46
Preparing and Running an Electrophoretic Assay.............................................................. 50
Analyzing and Evaluating the Results of an Electrophoretic Assay................................ 81
Result Flagging....................................................................................................................... 152
Running and Evaluating Flow Cytometric Assays...........................................................166
Principles of Flow Cytometric Measurements.................................................................. 167
Overview of Flow Cytometric Assays ................................................................................. 176

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Preparing and Running a Flow Cytometric Assay ............................................................ 179
Analyzing and Evaluating the Results of a Flow Cytometric Assay............................... 211
Working with Chip Data and Assays................................................................................258
2100 Expert Data Overview .................................................................................................. 259
Handling Assays..................................................................................................................... 262
Handling Chip Data................................................................................................................ 267
Organizing, Backing up, and Archiving 2100 Expert Data ............................................... 269
Importing Data........................................................................................................................ 271
Exporting Data........................................................................................................................ 277
Printing Reports ..................................................................................................................... 286
Configuring Tables................................................................................................................. 293
Administering System Functions ......................................................................................299
Configuring 2100 expert........................................................................................................ 300
Using Log Books .................................................................................................................... 310
Running Instrument Diagnostics ......................................................................................316
How to Run Instrument Diagnostics Tests........................................................................ 321
Performing Verifications....................................................................................................325
Products, Spare Parts, and Accessories..........................................................................334
Glossary ...............................................................................................................................338

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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.

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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 14 is meant for experienced users. It briefly summarizes the
necessary steps to prepare and run an assay.
•“Looking at 2100 Expert” on page 28 shows how to get started with the 2100 expert
software, and outlines its main operational possibilities.
•“Running and Evaluating Electrophoretic Assays” on page 45 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 166 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 258 shows you what to do to open, save,
import and export files, and how to print the results.
•“Administering System Functions” on page 299 is your guideline for configuring the
2100 expert software.
•“Running Instrument Diagnostics” on page 316 shows how to use the diagnostic tests
to check the bioanalyzer hardware for proper functioning.

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•“Performing Verifications” on page 325 describes how you can validate your
bioanalyzer system.
•“Products, Spare Parts, and Accessories” on page 334 lists all parts and
accessories—including reorder numbers—that are required for electrophoretic and
flow cytometric measurements.
•“Glossary” on page 338 explains terms in context with flow cytometry, electrophoresis,
and terms specific to the bioanalyzer software and hardware.
If you have any questions this manual cannot answer, please refer to the supplemental
literature listed in “Related Documents” on page 8. If you still have questions, contact
Agilent for additional support at:
http://www.agilent.com/chem/labonachip

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Related Documents
A collection of supplemental literature is given in the following.
Bioanalyzer Manuals
CD-ROM
Reagent Kit Guides
The Reagent Kit Guides give you information on how to perform specific assays,
including sample and chip preparation.
Publication Number Title
G2938-90006 Agilent 2100 Bioanalyzer Installation and Safety Manual
G2946-90003Agilent 2100 Bioanalyzer Maintenance andTroubleshooting
Guide
Publication Number Title
G2946-60002 Agilent 2100 Bioanalyzer – How to Use Multimedia CD-ROM
Publication Number Title
G2938-90300 Kit Guide Binder English (including all Reagent Kit Guides)
G2938-90010 Reagent Kit Guide DNA 500 and DNA 1000 Assay
G2938-90020 Reagent Kit Guide DNA 7500 and DNA 12000 Assay

Contents ▲9▼Index
Application Notes and Technical Notes
Application Notes and Technical Notes are available from the Agilent 2100 Bioanalyzer
Help Desk or from the lab-on-a-chip web pages:
http://www.agilent.com/chem/labonachip
Newly Published Documentation
Follow this link to see if there is any new documentation:
http://www.chem.agilent.com/scripts/Library.asp
G2938-90030 Reagent Kit Guide RNA 6000 Nano Assay
G2938-90040 Reagent Kit Guide RNA 6000 Pico Assay
G2938-90050 Reagent Kit Guide Protein 200 Plus Assay
G2938-90060 Reagent Kit Guide Protein 50 Assay
G2938-90070 Reagent Kit Guide Cell Fluorescence Assays
G2938-90080 Reagent Kit Guide Cell Fluorescence Checkout Kit
Publication Number Title

Contents ▲10 ▼Index
How to Use this Manual
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