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
No part of this manual may be reproduced in any form or by
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translation into a foreign language) without prior agreement
and written consent from Agilent Technologies, Inc. as
governed by United States and international copyright laws.
Manual Part number: G2946-90004
Edition: May 2005
Agilent Technologies
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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

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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

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How to Use this Manual
This manual uses convenient online navigation features and follows certain typographic
conventions.
Online Navigation
Use the interactive bookmarks in this
frame to move to your desired topic.
Use Acrobat Reader’s navigation bar
to move around within a topic.
Here is the current page number.
▲Displays the previous page.
▼Displays the next page.
Click here to go to the index.Click here to go to the table of contents.

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After you have chosen a topic with the bookmarks, use the buttons in Acrobat Reader’s
toolbar to move around within the topic.
Displays the first page.
Displays the last page.
Returns to the next view.
Click several times to redo
more view changes.
Returns to the previous view.
Click several times to undo
more view changes.
Displays the previous page.
Displays the next page.

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Layout Conventions
The following typographic conventions are used in this manual:
Highlight Meaning
Italic On-screen element
Example: ... the OK button.
Emphasis
Example: Right-click the ...
Term
Example: Dot plots show events as dots.
Reference to another document
Example: Refer to the Agilent 2100 Bioanalyzer Troubleshooting and
Maintenance Guide.
Blue Cross-reference or hyperlink
Examples:
“Introduction to the Key Features of the 2100 expert” on page 29
http://www.agilent.com/chem/labonachip
Courier Code
Example: .. the command line parameter
-port 2 ...
Courier
bold
User input
Example: Enter 50 MB.

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Safety Notices, Notes and Tips
Safety notices, notes and tips in this document have the following meaning:
WARNING
A warning notice denotes a hazard. It calls attention to an operating procedure,
practice, or the like that, if not correctly performed or adhered to, could result in
personal injury or death. Do not proceed beyond a warning notice until the indicated
conditions are fully understood and met.
CAUTION
A caution notice denotes a hazard. It calls attention to an operating procedure,
practice, or the like that, if not correctly performed or adhered to, could result in
damage to the product or loss of important data. Do not proceed beyond a caution
notice until the indicated conditions are fully understood and met.
NOTE
A note contains important, helpful, or additional information.
TIP
A tip usually points out a timesaving feature.

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Quick Start
The following step-by-step instructions guide you through a measurement with the
Agilent 2100 bioanalyzer.
Preparing the Agilent 2100 Bioanalyzer
1Ensure that the proper cartridge is installed in the bioanalyzer. You can identify the
installed cartridge by the number engraved at the front.
c= Electrode Cartridge for electrophoretic assays
d= Pressure Cartridge for flow cytometric assays
Engraved number
Note that there are also electrode cartridges
without an engraved number.

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2If you have to change the cartridge, follow the instructions in “Loading the
Electrophoresis Chip into the Bioanalyzer” on page 58 or “Loading the Cell Chip into the
Bioanalyzer” on page 189, respectively.
Switching on the Agilent 2100 Bioanalyzer
1Make sure the bioanalyzer is connected to line power and connected to the PC.
2Turn on the line switch at the rear of the instrument.
The status LED at the front of the bioanalyzer should light up.
Lid
Status LED

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The status LED shows you the current status of the instrument.
Running a Measurement
1To start the 2100 expert software on the connected PC, go to your desktop and
double-click the following icon:
Signal Meaning
Green light Instrument is switched on and ready for measurement.
Green blinking Measurement is running.
Orange blinking Instrument is busy (running self diagnostic, for example).
Red light Instrument is not ready for measurement. Switch the instrument off
and on again. If the problem persists, call Agilent service.

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After startup of the software, you enter the Instrument context:
NOTE
If you started 2100 expert for the first time after installation, you first need to activate
the different software modules with your license keys. See Figure ,“How to Activate
Software Licenses” for details.

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The Instrument tab shows you the status of the bioanalyzer:
2Make sure that a bioanalyzer has been detected before continuing.
Icons Meaning
Bioanalyzer detected, lid is open.
Bioanalyzer detected. Lid is closed, but no chip is inserted.
No bioanalyzer has been detected.
Check the COM Port setting (see figure under step 3), the RS 232
connection cable, the power cable, and the power switch. For
details on how to set up the bioanalyzer and connect it to a PC, see
Agilent 2100 Bioanalyzer Installation and Safety Guide.

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3Select an assay for the chip run.
On the Instrument tab, click the Assays button.
– OR –
Click the Assays menu.
Both will open a menu, allowing you to select an assay for the measurement.
Note that you can also select File > Open File to Run. This opens a dialog box allowing
you to load either an assay (.xsy) or a chip data file (.xad).
4Prepare the samples and the chip.
For detailed information on sample and chip preparation refer to:
–Reagent Kit Guides that are available for each reagent kit
–Application Notes that are available for specific kits and applications
NOTE
When preparing chip and samples, pay attention to the essential measurement
practices described in “Essential Measurement Practices (Electrophoretic Assays)”
on page 55 and “Essential Measurement Practices (Flow Cytometric Assays)” on
page 187 or as described in the respective Reagent Kit Guide.

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5Insert the chip in the Agilent 2100 bioanalyzer:
aOpen the lid.
The status of the bioanalyzer is updated on the Instrument tab.
bCheck that the cartridge is inserted properly and the chip selector is in the correct
position (“1” for electrophoretic assays, “2” for flow cytometric assays).
For details, please refer to “Loading the Electrophoresis Chip into the Bioanalyzer”
on page 58 or “Loading the Cell Chip into the Bioanalyzer” on page 189, respectively.