Agilent Technologies DP235 Guía de usuario

s1Agilent 2100 Bioanalyzer2100 Expert User’s GuideEdition November 03

Contents ▲ 10 ▼ IndexApplication Notes and Technical NotesApplication Notes and Technical Notes are available from the Agilent 2100 Bioanalyzer Help D

Contents ▲ 100 ▼ IndexData Analysis: ProteinThe data analysis process for protein assays consists of the following steps:1. Raw data is read and store

Contents ▲ 101 ▼ Index4. A sizing ladder (see the example electropherogram below), which is a mixture of proteins of different known sizes, is run fir

Contents ▲ 102 ▼ Index5. A standard curve of migration time versus size is plotted from the sizing ladder by interpolation between the individual prot

Contents ▲ 103 ▼ Index6. Two proteins are run with each of the samples, bracketing the sizing range. The “lower marker” and “upper marker” proteins ar

Contents ▲ 104 ▼ Index7. The standard curve, in conjunction with the markers, is used to calculate protein sizes for each sample from the migration ti

Contents ▲ 105 ▼ IndexSmear AnalysisThe 2100 expert software allows to perform a smear analysis for all electrophoresis assays. When the smear analysi

Contents ▲ 106 ▼ Index4 Under Smear Analysis select the checkbox Perform Smear Analysis.5 Click the Apply button that changes become effective.

Contents ▲ 107 ▼ IndexPerforming Smear AnalysisAfter enabling the smear analysis in the setpoint explorer, you are able to insert regions of interest

Contents ▲ 108 ▼ Index3 Repeat the previous step until the number of required regions are inserted. 4 Adjust the regions by directly moving the dashed

Contents ▲ 109 ▼ IndexNOTEThe smear analysis table can be directly edited by selecting the region table under Smear Analysis in the setpoint explorer.

Contents ▲ 11 ▼ IndexWhat’s New in 2100 ExpertProducts2100 expert is the successor to the Bio Sizing and Cell Fluorescence software.• 2100 expert prov

Contents ▲ 110 ▼ IndexIn the smear analysis table, you can edit the Region Start Size and Region End Size, for example:

Contents ▲ 111 ▼ IndexChanging the Data AnalysisDifferent sets of parameters (data analysis setpoints) can be changed in the software in order to modi

Contents ▲ 112 ▼ IndexAbout the Setpoint ExplorerThe tool allowing you to modify the data analysis setpoints is the Setpoint Explorer. The setpoint ex

Contents ▲ 113 ▼ IndexTo show the setpoint explorer, on the Electropherogram/Gel tab, click the vertical bar on the right edge of the application wind

Contents ▲ 114 ▼ IndexChanging any global setpoints while local settings have been applied opens a dialog box asking whether to override custom sample

Contents ▲ 115 ▼ IndexFiltering SetpointsThe first step the software takes in analyzing the raw data is to apply data filtering. The following filteri

Contents ▲ 116 ▼ IndexThe four peak find setpoints that can be changed are:Min Peak Height The Min Peak Height setpoint determines whether a peak is k

Contents ▲ 117 ▼ IndexManually Moving Fragment Start and End Points (RNA and Cy5-Labeled Nucleic Acids)It is also possible to alter the start and end

Contents ▲ 118 ▼ IndexTIPThe fragment table can be directly edited in the setpoint explorer:NOTEChanging the start or end points of the fragment will

Contents ▲ 119 ▼ IndexSetting the Baseline for Calculation of RNA ConcentrationAt low signal-to-noise ratios, the baseline that defines the area used

Contents ▲ 12 ▼ Index• 2100 expert has improved instrument control. Two bioanalyzers can be controlled at one time. It is possible to run measurements

Contents ▲ 120 ▼ IndexAssigning Upper and Lower Marker PeaksFor each DNA or protein sample, the upper and lower marker peaks are assigned first and th

Contents ▲ 121 ▼ IndexAligning or Unaligning the Marker Peaks (DNA or Protein assays only)The upper and lower are then aligned to the ladder markers b

Contents ▲ 122 ▼ IndexMarkers aligned to the ladderIf the sample marker peaks are either more than twice as far apart or less than half as far apart a

Contents ▲ 123 ▼ IndexNOTEWith DNA and protein assays, the height of marker peaks is assay dependent. Ladder peaks are analyzed to calculate a marker

Contents ▲ 124 ▼ IndexManual IntegrationFor all electrophoretic assays, the 2100 expert software allows to manually integrate peaks. Manual integratio

Contents ▲ 125 ▼ IndexThe baseline points become visible as blue or green dots. Highlighted baseline points are labelled green and can be moved either

Contents ▲ 126 ▼ Index4 Adjust the baseline points as appropriate.TIPTo move a peak baseline point along the vertical line, press the CTRL key and the

Contents ▲ 127 ▼ IndexExample: Removing peaksTo remove peaks:1 Highlight the Electropherogram tab in the Data and Assay context and zoom into the elec

Contents ▲ 128 ▼ Index3 Right-click on a baseline-point and select Remove Peak from the context menu. The two baseline points and the connecting line

Contents ▲ 129 ▼ IndexExample: Inserting peak baselinesTo insert peaks manually:1 Highlight the Electropherogram tab in the Data and Assay context and

Contents ▲ 13 ▼ IndexHow to Use this ManualThis manual uses convenient online navigation features and follows certain typographic conventions.Online N

Contents ▲ 130 ▼ Index2 Right-click on the electropherogram and select Add Peak from the context menu.

Contents ▲ 131 ▼ Index3 Two baseline points and the connecting line will appear and the integration results shown in the result and peak tables will b

Contents ▲ 132 ▼ IndexTIPBefore manual integration is done, it is strongly recommended to pause the automatic analysis and to restart it again when al

Contents ▲ 133 ▼ Index6 Click the Automatic Analysis button to enable the integration again. The integration results in the result and peak tables w

Contents ▲ 134 ▼ IndexReanalyzing a Chip Data FileNOTEOccasionally you may wish to open and view or reanalyze a chip data file that was run and saved

Contents ▲ 135 ▼ IndexRNA Assays Only:• Fragment names and colors associated with labels• Fragment start/end times, additional fragments (or delete fr

Contents ▲ 136 ▼ IndexComparing Samples from Different Electrophoretic Chip RunsThe 2100 expert software allows you to compare the measurement results

Contents ▲ 137 ▼ IndexThe .xad files appear in the Select Data Files list of the Tree View Panel.NOTEThe Select Data Files list also contains all elec

Contents ▲ 138 ▼ IndexA new comparison file appears in the upper part of the tree view containing the sample. The sample is selected and its electroph

Contents ▲ 139 ▼ Index5 You can now add further samples from any of the open .xad files to the comparison file.TIPDouble-clicking a sample name in the

Contents ▲ 14 ▼ IndexAfter you have chosen a topic with the bookmarks, use the buttons in Acrobat Reader’s tool bar to move around within the topic.Di

Contents ▲ 140 ▼ IndexThe following message appears if you try to add a sample of a .xad file which has the wrong assay type:6 You can also remove sam

Contents ▲ 141 ▼ Index7 When you have added all your samples you can select the Comparison Summary Tab which displays information on the comparison fi

Contents ▲ 142 ▼ Index8 To compare the electropherograms of samples, go to the Electropherogram tab, click Overlaid Samples in the toolbar (see “Data

Contents ▲ 143 ▼ Index9 Select the Gel tab to display a comparison of the gel-like images of the samples.Note that the Gel Tab has the same functional

Contents ▲ 144 ▼ IndexNOTEYou can re-open comparison files to review the comparison results, and to add/remove samples.

Contents ▲ 145 ▼ IndexResult FlaggingResult flagging can be used to assign a user-defined color code to a sample. This lets you easily identify sample

Contents ▲ 146 ▼ IndexTIPThe examples shown in this chapter are taken from the demo assay “Demo Protein 200 Plus.xsy”, that comes with the 2100 expert

Contents ▲ 147 ▼ IndexDefining Result Flagging RulesThe rules can be defined on the Result Flagging tab, which is available in the Data and Assay cont

Contents ▲ 148 ▼ IndexA result flagging rule consists of the following:• Label ExpressionAn optional description for the rule used to label samples me

Contents ▲ 149 ▼ IndexColor IndicationResult flagging shows:• On the Chip Summary Tab:The colors in the Result Flagging column show which sample match

Contents ▲ 15 ▼ IndexLayout ConventionsThe following typographic conventions are used in this manual:Highlight MeaningItalic On-screen elementExample:

Contents ▲ 150 ▼ Index• On the Gel Tab:The spot on top of the lane is colored if the sample matches a result flagging rule.• On the small gel image on

Contents ▲ 151 ▼ Index• On the Results tab:Result Flagging Color: color of the result flagging rule that the current sample matches.Result Flagging La

Contents ▲ 152 ▼ IndexTIPYou can export result flagging rules and import rules from other assay or chip data files. See “Exporting Result Flagging Rul

Contents ▲ 153 ▼ Index6 Enter an expression in the If Expression box. The expressions can be composed by making selections in the drop-down lists on t

Contents ▲ 154 ▼ IndexNOTEPlease refer to the function reference in the Help Pane (which appears when you select a function from the list) for details

Contents ▲ 155 ▼ IndexExample: Result FlaggingSample 1 contains 100 ng/µl proteins. The electropherogram shows 2 peaks for 2 different proteins, which

Contents ▲ 156 ▼ IndexRunning and Evaluating Flow Cytometric AssaysFor running and evaluating flow cytometric assays, you need to know the following:•

Contents ▲ 157 ▼ IndexPrinciples of Flow Cytometric MeasurementsBesides electrophoretic assays (DNA, RNA, and proteins), the Agilent 2100 bioanalyzer

Contents ▲ 158 ▼ IndexStaining CellsWith the 2100 expert software, you can differentiate several properties of a cell. The characteristics that are ex

Contents ▲ 159 ▼ IndexThe following dyes are recommended for use as the red stain:Dye (red fluorescence) Max. Excitation wavelengthMax. Emission wavel

Contents ▲ 16 ▼ IndexSafety Notices, Notes and TipsSafety notices, notes and tips in this document have the following meaning:WARNINGA warning notice

Contents ▲ 160 ▼ IndexCell Detection with the Agilent 2100 BioanalyzerLabChip technology allows cell measurements by integrating cell flow, hydrodynam

Contents ▲ 161 ▼ IndexMeasuring EventsThe bioanalyzer counts cells stained with fluorescent dyes and measures their fluorescence intensities. Each cel

Contents ▲ 162 ▼ IndexGenerating Histograms2100 expert counts the events, sorts them and displays them according to their fluorescence intensity in hi

Contents ▲ 163 ▼ IndexIn the histograms, the bar chart is replaced by a point-to-point line as shown in the following image.For detailed information,

Contents ▲ 164 ▼ IndexGenerating Dot PlotsSingle events can also be displayed related to both fluorescence values, generating a map of dot plots. In d

Contents ▲ 165 ▼ IndexIn predefined assays, the borders of the rectangular region represent the markers defined in the corresponding blue and red hist

Contents ▲ 166 ▼ IndexOverview of Flow Cytometric AssaysThe cell characteristic to be measured requires not only specific dyes. Several measurement pa

Contents ▲ 167 ▼ Index• Red to blueThis assay is for applications that apply a red reference dye and analyze blue fluorescent cells within a red popul

Contents ▲ 168 ▼ IndexThe regions of the dot plots are related to the markers of the histograms. Thus, the results of the dot plots are identical to t

Contents ▲ 169 ▼ IndexPreparing and Running a Flow Cytometric AssayA flow cytometric chip run requires the following steps:1. Set up and switch on the

Contents ▲ 17 ▼ IndexQuick StartThe following step-by-step instructions summarize the basic steps needed to perform a measurement with the Agilent 210

Contents ▲ 170 ▼ Index• Analyze and evaluate the results:– “Using Histograms for Evaluation” on page 199– “Using Dot Plots for Evaluation” on page 220

Contents ▲ 171 ▼ IndexSelecting a Flow Cytometric Assay for a Chip RunTo select an assay:1 Switch to the Instrument context.2 In the Tree View Panel,

Contents ▲ 172 ▼ Index3 If you do not see one of these icons, check that the bioanalyzer is switched on and properly connected:– Check the COM port se

Contents ▲ 173 ▼ IndexBoth will open the Assays menu, allowing you to select an assay from the submenus.– OR – Select File > Open File to Run... T

Contents ▲ 174 ▼ IndexNOTEAfter a chip run, the results can be evaluated using a different flow cytometric chip data or assay file. Refer to “Importin

Contents ▲ 175 ▼ Indexa Enter the number of samples you want to be measured.When preparing the chip (see “Preparing Samples and Chips for Flow Cytomet

Contents ▲ 176 ▼ IndexPreparing Samples and Chips for Flow Cytometric AssaysWARNINGSeveral substances such as dyes can have toxic, carcinogenic, or mu

Contents ▲ 177 ▼ IndexChip ReagentsSeveral reagents have to be added to the chip to prepare it for measurement. The following image shows which reagen

Contents ▲ 178 ▼ IndexEssential Measurement Practices (Flow Cytometric Assays)• Handle and store all reagents according to the instructions given in t

Contents ▲ 179 ▼ Index• Before bead preparation, vortex bead vials for 15 seconds.• Prepared chips must be used within 5 minutes. If a chip is not run

Contents ▲ 18 ▼ IndexSwitching on the Agilent 2100 Bioanalyzer1 Make sure the bioanalyzer is connected to line power and connected to the PC.2 Turn on

Contents ▲ 180 ▼ IndexLoading the Cell Chip into the BioanalyzerAfter preparing the chip, you can insert it into the Agilent 2100 bioanalyzer.NOTEBefo

Contents ▲ 181 ▼ Index3 Carefully close the lid. CAUTIONDo not force the lid closed. This may damage the pressure cartridge. The lid may not close com

Contents ▲ 182 ▼ IndexRunning a Flow Cytometric AssayRunning a flow cytometric assay in 2100 expert just means pressing a button.NOTEYou can stop a ch

Contents ▲ 183 ▼ IndexThe Dot Plot sub-tab shows single events (cells) as they are detected, displayed as dots. In the coordinate system, the red and

Contents ▲ 184 ▼ IndexThe status bar shows the name of the currently measured sample, a progress bar showing the measurement progress for the current

Contents ▲ 185 ▼ IndexFinishing the Chip RunWhen the measurements are finished, the End of run dialog box appears, showing you the number of samples t

Contents ▲ 186 ▼ IndexThe dialog box is closed.• If you selected Select file in Data Context, you are automatically taken to the Data and Assay contex

Contents ▲ 187 ▼ IndexStopping a Chip RunYou can stop a chip run at any time, for example, • if the quality of the measurement results does not meet y

Contents ▲ 188 ▼ IndexThe following message appears:2 Click Yes to stop the chip run.The End of Run dialog box appears.The measured samples are marked

Contents ▲ 189 ▼ Index3 If you want to immediately view the results in the Data and Assay context, select the Select file in Data Context check box.4

Contents ▲ 19 ▼ IndexRunning a Measurement1 To start the 2100 expert software on the connected PC, go to your desktop and double-click the following i

Contents ▲ 190 ▼ IndexEntering Chip, Sample, and Study Information During or after a chip run, you can document the run by entering information on chi

Contents ▲ 191 ▼ IndexNOTEYou may find some input fields already filled in, because chip, sample, and study information are taken over from the base a

Contents ▲ 192 ▼ IndexDisplaying the Measurement Results (Flow Cytometry)You can view the measurement results of a flow cytometric chip run as histogr

Contents ▲ 193 ▼ IndexHow to Switch Between Single View and Grid ViewTo switch between single view and grid view:1 From the Histogram or Dot Plot menu

Contents ▲ 194 ▼ IndexHow to Navigate Through the SamplesAt any time—even during a chip run—you can scroll though all samples—either in histogram or d

Contents ▲ 195 ▼ IndexHow to Change the Display of Histograms and Dot PlotsIn single view, it is possible to change the display of histograms and dot

Contents ▲ 196 ▼ IndexYou can perform several zoom steps in a row. When you have zoomed a histogram or dot plot, the Undo Zoom and Undo All buttons ar

Contents ▲ 197 ▼ IndexTo display data points in histograms:1 From the Histogram menu, select Show Data Points.All events are shown as bullets.To put a

Contents ▲ 198 ▼ IndexAnalyzing and Evaluating the Results of a Flow Cytometric AssayYou can analyze and evaluate result data of flow cytometric assay

Contents ▲ 199 ▼ IndexUsing Histograms for EvaluationHistograms are graphical representations of the measurement results, where the number of events (

Contents ▲ 2 ▼ IndexNotices© Agilent Technologies, Inc. 2000-2003No part of this manual may be reproduced in any form or by any means (including elect

Contents ▲ 20 ▼ IndexIn the upper left of the Instrument tab, an icon shows the status of the bioanalyzer:2 Make sure that a bioanalyzer has been dete

Contents ▲ 200 ▼ IndexMarkersMarkers are used to define a range of fluorescence intensity values in a histogram. The upper and lower limits of the ran

Contents ▲ 201 ▼ IndexGatingGating is used to restrict the number of events that are evaluated by gating out (filtering) events that do not have the f

Contents ▲ 202 ▼ Index• Gating from red to blue uses the red histogram to define the subset by a marker (GFP assay).NOTEPredefined assays have a fixed

Contents ▲ 203 ▼ IndexThe following figures illustrate gating from blue to red.The two histograms display all measured events in the blue histogram an

Contents ▲ 204 ▼ IndexBy setting a marker on the blue histogram, you can define the blue fluorescence range that must be met for a cell to be consider

Contents ▲ 205 ▼ IndexThe red histogram displays now only cells with blue and red fluorescence within the marker. To evaluate this subset, you can set

Contents ▲ 206 ▼ IndexThe following image shows two histograms with a gating direction from blue to red (left to right) of an apoptosis assay. The blu

Contents ▲ 207 ▼ IndexHow to Insert a Marker in a HistogramA marker is shown as two vertical lines that define a region of fluorescence values. It is

Contents ▲ 208 ▼ IndexYou can remove markers that you do not need any more:1 Click on one of the vertical lines in the histogram to select the marker.

Contents ▲ 209 ▼ IndexHow to Configure MarkersYou can change the color, name, and the upper and lower limits of the marker:1 Double-click the desired

Contents ▲ 21 ▼ Index3 Select an assay for the chip run.On the Instrument tab, click the Assay... button.– OR – Click the Assays menu.Both will open t

Contents ▲ 210 ▼ IndexNOTEThe lower and upper values must be within the range of 0.01 – 10000 relative fluorescence units.5 Click the Color button t

Contents ▲ 211 ▼ IndexHow to Move the Upper and Lower Limits of MarkersYou can change the position of both marker lines by dragging them with the mous

Contents ▲ 212 ▼ IndexHow to Copy Markers to All HistogramsOnce a marker is defined, you can copy it in the histograms of all samples (generic assays

Contents ▲ 213 ▼ IndexTo set the gating direction:1 Select the marker in the red or blue histogram you want to use as a gate for the other histogram.

Contents ▲ 214 ▼ IndexHow to Overlay HistogramsYou can compare samples by overlaying their gated histograms. This is useful, for example, if you want

Contents ▲ 215 ▼ IndexTo overlay all samples:1 Click the Overlaid Samples button to open a drop-down list.2 Select All Samples to overlay the histog

Contents ▲ 216 ▼ IndexHow to Set Signal Colors for Overlaid HistogramsYou can use the Graph Settings tab in the Options dialog box to configure the si

Contents ▲ 217 ▼ IndexDisplaying the Results of Histogram EvaluationsThe calculated results are displayed in result tables, one table below each histo

Contents ▲ 218 ▼ IndexThe content of the result tables depends on the gating direction. The histogram that is used for gating can display the followin

Contents ▲ 219 ▼ IndexThe histogram that displays the gated data can show the following data:Marker All events – this row shows the data for all event

Contents ▲ 22 ▼ Index4 Prepare the samples and the chip.For detailed information on sample and chip preparation refer to the– Reagent Kit Guides that

Contents ▲ 220 ▼ IndexUsing Dot Plots for EvaluationOn the Dot Plot tab, cells are displayed as dots, where their red fluorescence intensity is mapped

Contents ▲ 221 ▼ IndexHow to Add Regions to Dot Plots (Generic Assay only)You can draw regions in dot plots of generic assays. If there are regions al

Contents ▲ 222 ▼ IndexTo insert an existing region:1 Select the sample where you want to insert an existing region from another sample and click Inser

Contents ▲ 223 ▼ IndexHow to Configure RegionsYou can change the color of the region border, edit the region’s name, and define the position and size

Contents ▲ 224 ▼ Index3 Enter fluorescence values for the left, right, bottom, and top side of the rectangle to define position and size of the region

Contents ▲ 225 ▼ IndexHow to Change Position and Size of a RegionYou can change the size and position of regions to restrict the number of included ev

Contents ▲ 226 ▼ IndexTo change size and position numerically:1 Double-click the region to open the Configure Region dialog box.2 Enter fluorescence v

Contents ▲ 227 ▼ IndexClick No to create new regions that are not “connected”. The region will be inserted in the dot plots of all other samples. When

Contents ▲ 228 ▼ IndexDisplaying the Results of RegionsThe measurement results and calculations for regions are displayed in the result table below th

Contents ▲ 229 ▼ IndexEvaluating Antibody Staining, Apoptosis, and GFP AssaysWith the 2100 expert software, several predefined assays are supplied. Yo

Contents ▲ 23 ▼ Indexc Place the chip into the receptacle. The figure shows this for an electrophoresis chip.The chip fits only one way. Do not use fo

Contents ▲ 230 ▼ IndexEvaluating Antibody Staining AssaysAntibody staining lets you measure protein expression on the surface or inside a cell by mean

Contents ▲ 231 ▼ IndexHistogram EvaluationThe blue histogram is used for gating. High fluorescence in the blue histogram means that the cells are livi

Contents ▲ 232 ▼ IndexWhen using the calcein marker in the blue histogram for gating, only living cells are considered for building the histogram of t

Contents ▲ 233 ▼ IndexDot plot evaluationIf you switch to the Dot Plot tab, one region is displayed in the dot plot. The red fluorescence values of th

Contents ▲ 234 ▼ IndexThe results of the dot plot evaluation are numerically displayed in the result table:All measured eventsEvents covered by the re

Contents ▲ 235 ▼ IndexEvaluating Apoptosis AssaysThe apoptosis assay can be used to examine how many apoptotic cells are within a living cell populati

Contents ▲ 236 ▼ IndexHistogram evaluationThe two histograms displaying the results of the assay are related to calcein (blue fluorescence) and annexi

Contents ▲ 237 ▼ IndexWhen using the calcein marker in the blue histogram for gating, only the living cells are considered for building the red histog

Contents ▲ 238 ▼ IndexDot plot evaluationIf you switch to the Dot Plot tab, one region is displayed in the dot plot. The red fluorescence values of th

Contents ▲ 239 ▼ IndexThe results of the dot plot evaluation are displayed in the result table.All measured events Events covered by the regionAmount

Contents ▲ 24 ▼ IndexThe bioanalyzer icon changes to a chip icon (a DNA chip icon, for example):If the chip is not detected, open and close the lid ag

Contents ▲ 240 ▼ IndexEvaluating GFP AssaysWith GFP (Green Fluorescent Protein) assays, the fluorescent substance is not a dye, but a protein. Cells c

Contents ▲ 241 ▼ IndexThe values are displayed in the result table, each histogram has its own table.After gating by using the red histogram, in the b

Contents ▲ 242 ▼ IndexHigh fluorescence value indicates GFP-producing cellsAmount of all cells with high CBNF fluorescence selected by the red markerA

Contents ▲ 243 ▼ IndexDot plot evaluationIf you switch to the Dot Plot tab, one region is displayed in the dot plot. The red fluorescence values of th

Contents ▲ 244 ▼ IndexThe results of the dot plot evaluation are displayed in the result table.All measured events Events covered by the regionAmount

Contents ▲ 245 ▼ IndexWorking with Chip and Assay DataYou can make efficient use of the chip and assay data generated by the 2100 expert software, if

Contents ▲ 246 ▼ Index2100 Expert Data OverviewThe 2100 expert software manages data in the following different formats:• Assay files (.xsy)• Chip dat

Contents ▲ 247 ▼ Index• Ladder table and peak table (electrophoretic assays only)• Result flagging rules (electrophoretic assays only)Chip data filesC

Contents ▲ 248 ▼ IndexComparison filesYou can compare the measurement results from different chip runs (electrophoretic chip data files of same assay

Contents ▲ 249 ▼ IndexHandling AssaysPredefined AssaysPredefined assays are provided with 2100 expert. They are meant and prepared for measurements us

Contents ▲ 25 ▼ IndexThe chip run starts. The Raw Signals sub-tab shows an electropherogram of the currently measured sample. The name of the sample i

Contents ▲ 250 ▼ IndexTIPIf you just want to view the properties of a custom assay, you can open the assay file in read-only mode (see “Open” on page

Contents ▲ 251 ▼ IndexHow to Create a Custom AssayTo create a custom assay:1 Switch to the Data and Assay context.2 From the Assays menu, select an as

Contents ▲ 252 ▼ IndexHow to Modify a Custom AssayNOTEYou cannot save modifications to predefined assays such as Apoptosis or DNA 1000.To modify a cus

Contents ▲ 253 ▼ IndexHandling Chip DataChip data (.xad) files are automatically generated at the end of a chip run. The .xad files are given names th

Contents ▲ 254 ▼ IndexThe benefit of opening chip data files as read-only is to prohibit you or other users from making changes that would alter the f

Contents ▲ 255 ▼ IndexOrganizing, Retrieving, and Backing up 2100 Expert DataAs you begin to work with the 2100 expert software, it is good practice t

Contents ▲ 256 ▼ IndexImporting Data2100 expert allows to reprocess assays and chip run files from the Bio Sizing and Cell Fluorescence applications.

Contents ▲ 257 ▼ IndexImporting Bioanalyzer FilesNOTEBioanalyzer files imported and saved in the 2100 expert software can no longer be opened with the

Contents ▲ 258 ▼ IndexUpon importing, the file gets converted to a new 2100 expert file:Note that the new 2100 expert file inherits the name from the

Contents ▲ 259 ▼ IndexImporting Data Analysis SetpointsYou can import data analysis setpoints from other assay (.xsy) or chip data (.xad) files of the

Contents ▲ 26 ▼ IndexThe number of the sample that is currently being measured is indicated on the information bar:The status bar shows the name of th

Contents ▲ 260 ▼ Index4 Click Yes.NOTEImporting data analysis setpoints overwrites all current setpoint values.– All files: the setpoint values are up

Contents ▲ 261 ▼ IndexImporting Chip, Sample, and Study InformationOn the Sample Information and Study Information sub-tabs of the Chip Summary tab, y

Contents ▲ 262 ▼ IndexImporting Result Flagging RulesYou can import result flagging rules into electrophoretic assay (.xsy) or chip data (.xad) files.

Contents ▲ 263 ▼ IndexExporting Data2100 expert allows you to export the results of your chip runs in a variety of formats. The exported data can be u

Contents ▲ 264 ▼ IndexExporting Chip Run DataTo export chip run data:1 Switch to the Data and Assay context.2 In the Tree View Panel, select a chip da

Contents ▲ 265 ▼ IndexTIPChip run data can be automatically exported every time a chip run has finished. Refer to “Exporting Chip Run Data Automatical

Contents ▲ 266 ▼ IndexExporting Chip Run Data AutomaticallyNOTEKeep in mind that exporting a chip data file can require up to 20 MB of disk space. In

Contents ▲ 267 ▼ IndexExporting TablesYou can export:• Result tables, peak tables, fragment tables, and ladder tables as .csv files or .xls files.• Lo

Contents ▲ 268 ▼ Index3 Enter a file name and choose the destination directory.4 Under Export file format, select HTML file for .html output, or Tabbe

Contents ▲ 269 ▼ IndexExporting GraphsYou can export the following graphs as individual graphic files:• Gel-like image• Electropherogram• Electrophero

Contents ▲ 27 ▼ IndexFinishing the MeasurementWhen the measurement is finished, the End of run dialog box appears, showing you the status of the assay

Contents ▲ 270 ▼ IndexNote the following:• Histograms: only one histogram graph is exported, either the red or the blue histogram.• Electropherograms:

Contents ▲ 271 ▼ IndexPutting Graphs and Tables on the ClipboardYou can put the following items on the clipboard:• Gel-like image• Electropherogram• E

Contents ▲ 272 ▼ IndexTo put a graph or table on the clipboard:1 Right-click the graph or table (region).2 From the context menu, select Copy Gel/Copy

Contents ▲ 273 ▼ IndexExporting Chip, Sample, and Study InformationOn the Sample Information and Study Information sub-tabs of the Chip Summary tab, y

Contents ▲ 274 ▼ IndexExporting Result Flagging RulesYou can export result flagging rules for reuse in other electrophoretic assay (.xsy) or chip data

Contents ▲ 275 ▼ IndexPrinting ReportsFor documentation and presentation purposes, you can print reports for assay (.xsy), chip data (.xad), validatio

Contents ▲ 276 ▼ IndexHow to Print a Chip Run ReportThe following information can be included in a chip run report:• You can always include:– Assay su

Contents ▲ 277 ▼ IndexTo print a report:1 Switch to the Data and Assay context.2 In the Tree View Panel select a file, either an assay (.xsy) or a chi

Contents ▲ 278 ▼ Indexwells you would like to print, following the instructions as shown on the dialog box. Also refer to “Print (Electrophoresis)” on

Contents ▲ 279 ▼ IndexThe following example shows the “Run Summary” part of an RNA chip run report.

Contents ▲ 28 ▼ IndexThis takes you to the Data and Assay context, and the data file that has just been generated by your chip run is selected. The Ch

Contents ▲ 280 ▼ IndexHow to Turn on and Configure Automatic Printing of Chip Run ReportsA report can be printed (or generated) automatically at the e

Contents ▲ 281 ▼ Index4 Adjust the settings:– Under Print Item, select the options that should be contained in the report.– Under Save To File, you ca

Contents ▲ 282 ▼ IndexConfiguring Tables2100 expert uses various tables to present data:• Result tables• Peak tables• Fragment tables• Log book tables

Contents ▲ 283 ▼ IndexShowing and Hiding ColumnsTo add the Aligned Migration Time column to the table:1 Right-click the heading row of the table.2 Fro

Contents ▲ 284 ▼ Index3 Move Aligned Migration Time from the Available list to the Displayed list by clicking the single-arrow button.4 Click OK.A new

Contents ▲ 285 ▼ IndexChanging the Column SequenceTIPYou can set the column sequence also using the Up and Down buttons in the Configure Columns dialo

Contents ▲ 286 ▼ IndexChanging the Table HeightTo increase or reduce the table height:1 Position the mouse pointer above the heading row of the table

Contents ▲ 287 ▼ IndexReading the Log Books2100 expert provides two log books:Run LogThe run log table contains events generated during a chip run, in

Contents ▲ 288 ▼ IndexPlease refer to “System Log Viewer” on page 561 for more details on the system log table.The system log is saved in the file “Sy

Contents ▲ 289 ▼ IndexHow to Change the Display of the Log BooksTo sort a log book table:1 Right-click any table column.2 From the context menu, selec

Contents ▲ 29 ▼ Index2 In the tree view panel, click any sample name, or the ladder.This selects the Electropherogram tab, which displays a data plot

Contents ▲ 290 ▼ IndexThe filter definition in the following example would exclude all events from the log book table with an Event Type other than Cr

Contents ▲ 291 ▼ IndexTIPYou can hide/show any of the log table columns, and re-sort the columns by right-clicking the table and selecting Columns...

Contents ▲ 292 ▼ IndexNOTEThe search is not case-sensitive.4 To continue the search, click Find Next.

Contents ▲ 293 ▼ IndexConfiguring 2100 ExpertThe 2100 expert software can be configured as follows.• The names of data files can be generated automati

Contents ▲ 294 ▼ IndexHow to Specify Data File Names and DirectoriesThe measurement results are stored automatically when the chip run is complete. To

Contents ▲ 295 ▼ Index2 Select the check boxes of the strings you want to insert in the file names:To specify the directory where the chip data files

Contents ▲ 296 ▼ IndexHow to Set the Acoustic Chip AlertWhen a chip run has finished, you have to remove the chip from the bioanalyzer. You can activa

Contents ▲ 297 ▼ Index3 Select Off to turn off the alert sound.– OR –Select Default sound to use the standard alert sound.– OR –Select Custom Sound to

Contents ▲ 298 ▼ IndexHow to Specify Graph SettingsYou can compare measurement results of samples by overlaying their electropherograms or histograms.

Contents ▲ 299 ▼ IndexHow to Use the Advanced SettingsYou can use 2100 expert’s advanced settings to:• Automate starting, documenting, and archiving o

▲ 3 ▼ IndexContentsAbout this Manual ...

Contents ▲ 30 ▼ IndexWhat You Can do When the Measurement is FinishedWhen the measurement is finished, you can:• Document your chip run by entering sa

Contents ▲ 300 ▼ IndexTo modify the advanced settings:1 Select Tools > Options... to display the Options dialog box.2 Click the Advanced tab to bri

Contents ▲ 301 ▼ IndexNOTEIn addition to the regular chip data file (.xad), 2100 expert creates another raw data backup file (packet file: .pck) with

Contents ▲ 302 ▼ IndexNOTEThe Auto Print and Auto Export settings are independent from those made via the Export or Print command of the File menu.8 C

Contents ▲ 303 ▼ IndexRunning Instrument Diagnostics2100 expert provides several tests to check proper functioning of the bioanalyzer hardware. You sh

Contents ▲ 304 ▼ IndexElectrode Cartridge TestsFan Test Checks if the fan is running at the appropriate speed.Temperature Test Checks if the temperatu

Contents ▲ 305 ▼ IndexPressure Cartridge TestsHigh-Voltage Accuracy on Load TestCheck of channel-reference diode in transmission direction.Autofocus T

Contents ▲ 306 ▼ IndexNOTEWith bioanalyzer model G2938A only diagnostic tests in combination with the electrode cartridge can be performed.Test C hi p

Contents ▲ 307 ▼ IndexTest Chip Kit for Flow Cytometry Assays (reorder no. G2938-68200)Electrode/Diode Test Chip Can be used multiple times. 1Leak Cur

Contents ▲ 308 ▼ IndexHow to Run Instrument Diagnostics TestsNOTEDiagnostics tests cannot be run while the 2100 expert software is performing a chip r

Contents ▲ 309 ▼ Index4 Select the tests you want to run:– Select the Apply check boxes to select single tests.– Click Select All to select all availa

Contents ▲ 31 ▼ IndexLooking at 2100 ExpertBefore you begin with running assays on the Agilent 2100 bioanalyzer you should familiarize yourself with t

Contents ▲ 310 ▼ Index6 Follow the instructions given by the 2100 expert software. For example, exchange the cartridge, or put a test chip in the rece

Contents ▲ 311 ▼ IndexThe Status column indicates the status of each test:– Executing– Execution pending– Executed, passed– Executed, failed7 If any t

Contents ▲ 312 ▼ IndexPerforming QualificationsTo ensure a validated Agilent 2100 bioanalyzer system, qualification steps have to be performed at inst

Contents ▲ 313 ▼ IndexOperational QualificationOperational qualification proves that the bioanalyzer system is suitable for its intended use, that is,

Contents ▲ 314 ▼ IndexValidation ProcedureTo perform qualification tests:1 Switch to the Validation context.2 From the File menu select New.3 A New Va

Contents ▲ 315 ▼ Index6 In the Tree View Panel, navigate to the test category you want to execute. Select the category via IQ/OQ – SW/HW – PC name/Bio

Contents ▲ 316 ▼ IndexThe Save As dialog box appears.8 Specify a name and location for the validation results file (.xvd) and click Save.The selected

Contents ▲ 317 ▼ Index10Click OK.11The Status column shows whether the tests have been run successfully or not. For details on the Configuration tab,

Contents ▲ 318 ▼ Index12To view details on test execution, select the Results tab.For details on the Results tab, please refer to “Results Tab” on pag

Contents ▲ 319 ▼ Index15When you close the validation results file (File > Close), try to switch to another context or exit 2100 expert, the follow

Contents ▲ 32 ▼ IndexStarting 2100 ExpertTo start 2100 expert:1 Go to your desktop and double-click the following icon:– OR –From the Windows Start me

Contents ▲ 320 ▼ Index2100 Expert Software ReferenceThe 2100 expert software reference is organized as follows:• 2100 Expert Application Window Elemen

Contents ▲ 321 ▼ Index2100 Expert Application Window ElementsThe 2100 expert application window has the following regions (Data and Assay context):

Contents ▲ 322 ▼ IndexRegion PurposeTitle Bar Bar at the top of the window providing information on the application that you have started, and the ass

Contents ▲ 323 ▼ IndexTitle BarIf you are in the Data and Assay context, name and path of the current chip data or assay file are displayed on the tit

Contents ▲ 324 ▼ IndexAssays Menu Lets you open assay files for editing (Data and Assay context).Lets you select an assay for a chip run (Instrument c

Contents ▲ 325 ▼ IndexNOTENot all menus are visible at the same time. The Electropherogram menu, for example, is only available if electropherograms (

Contents ▲ 326 ▼ IndexFile MenuThe File menu provides functions for file handling and printing.Data and Assay Context

Contents ▲ 327 ▼ IndexFile menu item FunctionOpen... Brings up the Open dialog box, allowing you to open a chip data (.xad) or assay (.xsy) file. Mult

Contents ▲ 328 ▼ IndexPrint... Displays the Print (Flow Cytometry) or Print (Electrophoresis) dialog box, allowing you to generate various printouts o

Contents ▲ 329 ▼ IndexInstrument ContextFile menu item FunctionOpen File to Run... Brings up the Open dialog box, allowing you to select a chip data (

Contents ▲ 33 ▼ Index2100 Expert Work AreaThe 2100 expert work area has standard elements such as pull-down menus and toolbars, and the main working a

Contents ▲ 330 ▼ IndexValidation ContextFile menu item FunctionNew Begins a new validation and inserts a New Validation item in the tree view.Open...

Contents ▲ 331 ▼ IndexComparison ContextPrint... Displays the Print (Validation) dialog box, allowing you to generate various reports on qualification

Contents ▲ 332 ▼ IndexFile menu item FunctionOpen... Brings up a system dialog box allowing you to open a comparison (.xac) or chip data (.xad) file.C

Contents ▲ 333 ▼ IndexContext MenuThe Context menu lets you switch between the four program modes, called “contexts”:The checkmark indicates the activ

Contents ▲ 334 ▼ IndexView MenuThe View menu provides functions to switch between the Gel/Electropherogram and Histogram/Dot Plot views, and between s

Contents ▲ 335 ▼ IndexData and Assay context (flow cytometric assay selected)View menu item FunctionHistogram Switches to the Histogram Tab (Single/Gr

Contents ▲ 336 ▼ IndexInstrument contextValidation/Comparison contextView menu item FunctionSingle View Switches to the Instrument Tab (Single View) o

Contents ▲ 337 ▼ IndexAssays MenuFrom the Assays menu, you can open assay files for editing (Data and Assay context). In the Instrument context, you c

Contents ▲ 338 ▼ IndexElectrophoresis – RNA All assays located in the ”..\assays\electrophoresis\RNA” folder are listed here. By default, these are:•

Contents ▲ 339 ▼ IndexFlow Cytometry All assays located in the ”..\assays\flow cytometry” folder are listed here. By default, these are:• Antibody Sta

Contents ▲ 34 ▼ IndexThe 2100 expert software can be operated in four modes, called “contexts”:• Instrument Context• Data and Assay Context• Validatio

Contents ▲ 340 ▼ IndexDemo – Flow Cytometry All assays located in the ”..\assays\demo\flow cytometry” folder are listed here. By default, these are:•

Contents ▲ 341 ▼ IndexDemo – Electrophoresis All assays located in the ”..\assays\demo\electrophoresis” folder are listed here. Demo Cy5 Labeled Nucle

Contents ▲ 342 ▼ IndexGel MenuGel menu item FunctionAutomatic AnalysisStarts automatic analysis. Peaks are detected, and the Peak Table gets calculate

Contents ▲ 343 ▼ IndexDon’t Analyze Analysis is switched off. Raw data is displayed on the Gel tab and the Peak Table is cleared.Previous Sample Highl

Contents ▲ 344 ▼ IndexGel Color Opens a submenu from which you can select a predefined foreground/background color scheme to be used for displaying th

Contents ▲ 345 ▼ IndexElectropherogram Menu

Contents ▲ 346 ▼ IndexElectropherogram menu itemFunctionAutomatic Analysis Starts automatic analysis. Peaks are detected, and the Peak Table gets calc

Contents ▲ 347 ▼ IndexScaling Mode Opens a submenu from which you can select one of the following modes:• Individual ScaleEach graph uses its own scal

Contents ▲ 348 ▼ IndexGraph Mode Lets you select one of the following click-and-drag operations on electropherograms: • ZoomMagnifies the correspondin

Contents ▲ 349 ▼ IndexCopy ElectropherogramPuts a copy of the electropherogram into the clipboard (single-well view). In multi-well view, all electrop

Contents ▲ 35 ▼ IndexNOTEMenus, toolbars, the tree view, and the main working area (tabs) significantly change when you switch between the contexts.An

Contents ▲ 350 ▼ IndexOverlaid Samples Lets you overlay electropherograms from multiple wells (single-well view only). Each electropherogram will be s

Contents ▲ 351 ▼ IndexHistogram MenuSingle View

Contents ▲ 352 ▼ IndexHistogram menu itemFunctionView Single Sample Displays the current histogram in single view.View All Samples Switches to the gri

Contents ▲ 353 ▼ IndexOverlaid Samples Lets you overlay histograms from multiple samples (single view only). Each histogram will be shown in a differe

Contents ▲ 354 ▼ IndexGate in Red histogramUses the selected marker of the blue histogram for gating in the red histogram (generic assays only).Insert

Contents ▲ 355 ▼ IndexGrid ViewIn grid view, the Histogram menu has the following commands, which work the same way as in single view (see above):

Contents ▲ 356 ▼ IndexDot Plot MenuSingle View

Contents ▲ 357 ▼ IndexDot Plot menu item FunctionSingle View Displays the current dot plot in single view.Grid View Switches to the grid view and high

Contents ▲ 358 ▼ IndexInsert Region into all dot plotsCopies the selected region into all other dot plots of the chip run (generic assays only).Insert

Contents ▲ 359 ▼ IndexGrid ViewIn grid view, the Dot Plot menu has the following commands, which work the same way as in single view (see above):Resul

Contents ▲ 36 ▼ IndexInstrument ContextOn startup, 2100 expert enters the Instrument context, where you can run DNA, RNA, protein or cell assays by se

Contents ▲ 360 ▼ IndexLog Book MenuResult flagging menu item FunctionLoad Rules Opens a system dialog box allowing you to load a set of result flaggin

Contents ▲ 361 ▼ IndexInstrument MenuLog Book menu item FunctionFind Opens the Find dialog box allowing you to search the run log table for any string

Contents ▲ 362 ▼ IndexTile MenuThe Tile menu is available if the Instrument Tab (Grid View) is displayed:Tile menu item FunctionTile Horizontal Arrang

Contents ▲ 363 ▼ IndexTools MenuTools menu item FunctionSystem Log Opens the System Log Viewer dialog box showing system-wide events in the system log

Contents ▲ 364 ▼ IndexWindows MenuIn the Data and Assay context, the Windows menu lets you switch between all open chip data (.xad) and assay (.xsy) f

Contents ▲ 365 ▼ IndexIf an assay is already selected for an instrument, the assay name appears instead of the instrument name.Help MenuHelp menu item

Contents ▲ 366 ▼ IndexOnline Store Takes you to the Life Sciences/Chemical Analysis Online Store (Internet connection required).About 2100 expert... D

Contents ▲ 367 ▼ IndexToolbarsThe toolbars are located below the menu bar and give you quick access to often required functions. TIPMove the mouse cur

Contents ▲ 368 ▼ IndexInstrument Context ToolbarButton FunctionSelect an item from this list to switch to another context.Brings up the Open dialog bo

Contents ▲ 369 ▼ IndexData and Assay Context – Electrophoresis ToolbarButton FunctionSelect an item from this list to switch to another context.Brings

Contents ▲ 37 ▼ IndexNOTEIf two bioanalyzers are connected to your PC, you can run both in parallel. During the chip run(s), you can view the status o

Contents ▲ 370 ▼ IndexGel ViewStarts automatic analysis. Peaks are detected, and the Peak Table gets calculated. Results are getting recalculated when

Contents ▲ 371 ▼ IndexElectropherogram ViewOpens a system dialog box allowing you to save the gel graph (all samples) as an image in JPEG (.jpg), Wind

Contents ▲ 372 ▼ IndexStarts automatic analysis. Peaks are detected, and the Peak Table gets calculated. Results are getting recalculated whenever cha

Contents ▲ 373 ▼ IndexLets you select one of the following scaling modes: • Individual ScaleEach graph uses its own scaling which is optimized for tha

Contents ▲ 374 ▼ IndexShows/hides the data points used to generate the electropherogram. Data points are visible only in the single-well view. Data po

Contents ▲ 375 ▼ IndexLets you overlay electropherograms from multiple wells (single-well view only). Each electropherogram will be shown in a differe

Contents ▲ 376 ▼ IndexData and Assay Context – Flow Cytometry ToolbarButton FunctionSelect an item from this list to switch to another context.Brings

Contents ▲ 377 ▼ IndexHistogram ViewDisplays the current histogram in single view.Switches to the grid view and highlights the current histogram.Undoe

Contents ▲ 378 ▼ IndexLets you overlay histograms from multiple samples (single view only). Each histogram will be shown in a different color and a co

Contents ▲ 379 ▼ IndexDot Plot ViewUses the selected marker of the blue histogram for gating in all red histograms (generic assays only).Uses the sele

Contents ▲ 38 ▼ IndexData and Assay ContextIn the Data and Assay context, you can • view, analyze, and evaluate the results of your chip runs that are

Contents ▲ 380 ▼ IndexPuts a copy of the selected dot plot into the clipboard.Opens a system dialog box allowing you to save the selected dot plot as

Contents ▲ 381 ▼ IndexData and Assay Context – Result Flagging ToolbarColors the dots inside the selected region using the color of the region border.

Contents ▲ 382 ▼ IndexData and Assay Context – Log Book ToolbarNOTEThe Log Book toolbar is also available in the System Log Viewer dialog box. See “Sy

Contents ▲ 383 ▼ IndexValidation Context ToolbarButton FunctionSelect an item from this list to switch to another context.Begins a new validation and

Contents ▲ 384 ▼ IndexComparison Context ToolbarNOTEIf a sample is selected in the comparison context, also the Gel or Electropherogram toolbar is ava

Contents ▲ 385 ▼ IndexInformation BarThe information bar is located below the toolbar.Instrument contextIf no chip run is in progress, the information

Contents ▲ 386 ▼ IndexData and Assay contextIf the Gel, Electropherogram, Histogram or Dot Plot tab is selected, you see the tab name followed by the

Contents ▲ 387 ▼ IndexIf you stopped a validation run, the information bar looks as follows:If you re-open a validation results file for review, no mo

Contents ▲ 388 ▼ IndexContext BarThe context bar is located on the left-hand side of the application window.By clicking the icons on the context bar,

Contents ▲ 389 ▼ IndexTree View PanelThe tree view panel is located on the left-hand side of the application window.TIPTo get more screen space in the

Contents ▲ 39 ▼ IndexValidation ContextThe Validation context is used to run and document qualification tests.For both the bioanalyzer hardware and so

Contents ▲ 390 ▼ IndexWhen a chip run has finished, a green checkmark appears:If the run was aborted or an error occurred, a red cross appears instead

Contents ▲ 391 ▼ IndexData and Assay ContextIn the Data and Assay context you can use the tree view to navigate through all open chip data (.xad) and

Contents ▲ 392 ▼ Index• Clicking a plus or minus sign next to a chip icon expands or collapses the sample list. • Clicking a chip data or assay item d

Contents ▲ 393 ▼ IndexValidation ContextIn the Validation context you can use the tree view to:• Navigate through validation results files.Clicking a

Contents ▲ 394 ▼ IndexNOTEItems “inherit” the symbol (status) of their “child(s)”. For example, if a single test fails, the whole validation will be m

Contents ▲ 395 ▼ IndexNOTEThe Select Data Files list also contains all electrophoretic .xad files that have been opened in the Data and Assay context.

Contents ▲ 396 ▼ IndexIn the upper part of the tree view, right-clicking a xac. file name opens a context menu with the following functionsIf you righ

Contents ▲ 397 ▼ IndexIn the lower part of the tree view, right-clicking a sample name opens a context menu with the following functions:TIPDouble-cli

Contents ▲ 398 ▼ IndexLower PanelThe lower panel is located in the lower left corner of the application window. It is available in the Data and Assay

Contents ▲ 399 ▼ IndexSmall Gel ViewIf the Electropherogram Tab (Single/Grid View) is displayed, the lower panel shows a small gel view (all wells).On

Contents ▲ 4 ▼ IndexResult Flagging...

Contents ▲ 40 ▼ IndexComparison ContextIn the Comparison context, you can open multiple electrophoretic chip data files and compare samples of the sam

Contents ▲ 400 ▼ IndexWhen a new chip run begins, the small gel view is blank and the first lane—the ladder well—is selected. As data is acquired, the

Contents ▲ 401 ▼ IndexTa bsThe main working area contains several tabs. These tabs are specific to the context you are working in:• Tabs (Instrument C

Contents ▲ 402 ▼ IndexInstrument Tab (Grid View)PurposeShows “live” electropherograms and/or dot plots, allowing you to watch data acquisition on two

Contents ▲ 403 ▼ IndexElementsBoth panels are labeled with name of the assay and the currently measured sample.For a detailed description of the “live

Contents ▲ 404 ▼ IndexInstrument Tab (Single View)PurposeThe Instrument tab lets you configure and start a chip run. During the chip run, you can watc

Contents ▲ 405 ▼ IndexElementsThe icon on the left-hand side shows the current status of the Agilent 2100 bioanalyzer:Icon MeaningA chip is detected a

Contents ▲ 406 ▼ IndexThe following information read from the instrument is for your information:Indicates that no bioanalyzer has been detected. Chec

Contents ▲ 407 ▼ IndexThe following controls let you select, start, and control a chip run.Control MeaningCOM Port Allows you to select a bioanalyzer

Contents ▲ 408 ▼ IndexChip Setup Sub-tabOn the Chip Setup sub-tab, you can specify a destination for the chip data file, and make data acquisition set

Contents ▲ 409 ▼ IndexFurther settings can be made for flow cytometric assays:Default Enable this option if you want to use the default time for measu

Contents ▲ 41 ▼ IndexRunning a Demo Assay2100 expert provides demo assays that you can use for a first impression of chip runs and data evaluation, ev

Contents ▲ 410 ▼ IndexRaw Signals Sub-tabDuring an electrophoretic chip run, the Raw Signals sub-tab shows an electropherogram of the currently measur

Contents ▲ 411 ▼ IndexDot Plot Sub-tabDuring a flow cytometric chip run, the Dot Plot sub-tab shows single events (cells) as they are detected, displa

Contents ▲ 412 ▼ IndexDiagnostics TabOn the Diagnostics tab, you can select and start hardware diagnostics tests on the selected bioanalyzer. The test

Contents ▲ 413 ▼ IndexInstrument InformationAt the top of the Diagnostics tab, the following information on the selected bioanalyzer is shown:Availabl

Contents ▲ 414 ▼ IndexBioanalyzer TestsElectrode Cartridge TestsElectronics Test Verifies proper functioning of all electronic boards in the bioanalyz

Contents ▲ 415 ▼ IndexPressure Cartridge TestsHigh-Voltage Stability Te stTests high voltage accuracy and stability of all 16 high voltage power suppl

Contents ▲ 416 ▼ IndexCommand buttonsTest PropertiesIn this area, you can see details (such as name, description, limits and requirements) on the test

Contents ▲ 417 ▼ IndexTabs (Data and Assay Context)In the Data and Assay context, the following tabs are available:• Assay Properties Tab lets you dis

Contents ▲ 418 ▼ IndexAssay Properties TabPurposeOn this tab, you can display and modify parameters (setpoints) of the current assay or chip data file

Contents ▲ 419 ▼ IndexFlow Cytometric AssaysAccessThe Assay Properties tab is always available in the Data and Assay context.

Contents ▲ 42 ▼ IndexThis opens a menu, allowing you to select an assay from submenus.4 Select a demo assay, for example Demo > electrophoresis >

Contents ▲ 420 ▼ IndexElementsAssay Icon This icon visualizes the assay type.Electrophoretic AssaysDNARNAProtein

Contents ▲ 421 ▼ IndexFlow Cytometric AssaysApoptosis/Red to BlueAntibody Staining/Blue to RedGFP (Green Fluorescence Protein)Generic/Checkout Beadssi

Contents ▲ 422 ▼ IndexFile Name Name of the assay (.xsy) file the current assay or chip data file is based on; .csy or .asy file if the basis is a Bio

Contents ▲ 423 ▼ IndexAnalysis sub-tab Shows a selection of characteristic assay parameters.Ladder sub-tab (electrophoretic assays only)Ladder peak ta

Contents ▲ 424 ▼ IndexFragments sub-tab (RNA assays only)Number: order in which the fragments are detected.Fragment Name: user-assigned or predefined

Contents ▲ 425 ▼ IndexSetpoint ExplorerLets you modify assay parameters (data analysis setpoints) globally, that is, for all samples. Click the + node

Contents ▲ 426 ▼ IndexTIPWhen applying modified data analysis setpoints, the software will (by default) immediately recalculate the raw data, which ta

Contents ▲ 427 ▼ IndexChip Summary TabPurposeThe Chip Summary tab shows information on the selected assay or chip data file, and lets you enter commen

Contents ▲ 428 ▼ IndexAccessThe Chip Summary tab is available in the Data and Assay context.ElementsNOTEIf you try to exit the Chip Summary tab after

Contents ▲ 429 ▼ IndexSample Information sub-tab (electrophoretic assays)The sample table includes:Sample Name Lets you enter easy-to-remember names f

Contents ▲ 43 ▼ IndexThe demo chip run starts and you can watch its progress on the Raw Signals tab, where you can see a simulation of data acquisitio

Contents ▲ 430 ▼ IndexRest. Digest (DNA only) Indicating that a sample is a restriction digest allows 2100 expert to note the possible comigration of

Contents ▲ 431 ▼ IndexSample Information sub-tab (flow cytometric assays)The sample table shows you the main measurement results and allows you to ent

Contents ▲ 432 ▼ IndexBlue Staining Lets you enter the name of the dye that is used for blue fluorescence staining.Red Staining Lets you enter the nam

Contents ▲ 433 ▼ IndexStudy Information sub-tabTo identify your assays easily, you can add information about the study (Study Name and Study Comments)

Contents ▲ 434 ▼ IndexInstrument Information sub-tabThis tab displays the temperature of the chip base plate recorded during the chip run. The acquisi

Contents ▲ 435 ▼ IndexStandard Curve sub-tab (DNA/Protein assays only)A standard curve of migration time versus size is plotted from the sizing ladder

Contents ▲ 436 ▼ IndexStandard Curve sub-tab (RNA assays only)A standard curve of mobility vs. size in logarithmic scale is plotted from the RNA sizin

Contents ▲ 437 ▼ IndexCalibration Curve sub-tab (protein assays only)If a standard protein was added on the chip and you have selected the option Use

Contents ▲ 438 ▼ IndexGel TabPurposeThe Gel tab shows gel-like images of the ladder and of all samples of a chip.On sub-tabs below the gel-like image,

Contents ▲ 439 ▼ IndexAccessThe Gel tab is always available • in the Data and Assay context if an electrophoretic chip data (.xad) file is selected, •

Contents ▲ 44 ▼ IndexAt the end of the simulation, the End of run dialog box appears. 6 Select the Select file in Data Context check box and click OK.

Contents ▲ 440 ▼ IndexWhen a new chip run starts, the gel view is blank and the first lane—the ladder well—is selected. As data is acquired, the selec

Contents ▲ 441 ▼ IndexThe dividing line between the gel graphs and the sub-tabs at the bottom can be moved in the vertical direction, giving more or l

Contents ▲ 442 ▼ IndexResults sub-tabFor DNA and protein assays, the Number of peaks found is shown.For protein assays, also the total relative concen

Contents ▲ 443 ▼ IndexThe analyzed data depends on the assay type:• DNADefault table columns are:Peak Number (leftmost column)The order in which the p

Contents ▲ 444 ▼ Index• RNADefault table columns are:• ProteinDefault table columns are:Peak Number (leftmost column)The order in which the peaks were

Contents ▲ 445 ▼ IndexNOTEYou can include further columns and also exclude columns from the peak table. Right-click the heading row of the table and s

Contents ▲ 446 ▼ IndexContext menuWhen you right-click the peak table, the following menu appears:The following functions are available:Calibration pr

Contents ▲ 447 ▼ IndexScale to Selected Peak (electropherograms only)Adapts the scale of the Y axis. The selected peak is displayed at maximum height.

Contents ▲ 448 ▼ IndexFragment Table sub-tab (RNA assays only)For each peak (rows), the table shows results for the predefined/specific fragments.Defa

Contents ▲ 449 ▼ IndexNOTEYou can include further columns and also exclude columns from the fragment table. Right-click the heading row of the table a

Contents ▲ 45 ▼ IndexClosing 2100 ExpertTo close 2100 expert:1 From the File menu, select Exit.2100 expert quits.However, if a chip run is in progress

Contents ▲ 450 ▼ IndexSetpoint ExplorerTo show the setpoint explorer, click the vertical bar on the right edge of the application window:The setpoint

Contents ▲ 451 ▼ IndexElectropherogram Tab (Single/Grid View)PurposeThe Electropherogram tab shows electropherograms of all samples (including the lad

Contents ▲ 452 ▼ IndexSingle ViewAccessThe Electropherogram tab is always available • in the Data and Assay context if an electrophoretic chip data (.

Contents ▲ 453 ▼ IndexElectropherogram ViewIn Grid View, you see electropherograms of all samples (including ladder) at the same time. The electropher

Contents ▲ 454 ▼ IndexMoving the mouse pointer over a curve in an electropherogram shows the sample name and number. This is especially useful in over

Contents ▲ 455 ▼ IndexThe dividing line between the electropherogram graphs and the sub-tabs can be moved in the vertical direction, giving more or le

Contents ▲ 456 ▼ IndexCopy ElectropherogramPuts a copy of the electropherogram into the clipboard (single-well view). In multi-well view, all electrop

Contents ▲ 457 ▼ IndexWhen you right-click the top of a peak, the following menu appears:The following functions are available:Scale to Selected PeakA

Contents ▲ 458 ▼ IndexLegend sub-tabTo compare samples, you can overlay electropherograms from multiple samples (single view only). Each electropherog

Contents ▲ 459 ▼ IndexResults, Peak Table, and Fragment Table sub-tabsThe sub-tabs Results, Peak Table, and Fragment Table work exactly in the same wa

Contents ▲ 46 ▼ IndexAlso the following dialog box may appear:NOTEThis dialog box may also appear if you try to switch between contexts but there is u

Contents ▲ 460 ▼ IndexHistogram Tab (Single/Grid View)PurposeHistograms are plots of fluorescence intensity against the number of detected events (det

Contents ▲ 461 ▼ IndexSingle ViewAccessThe Histogram tab is always available in the Data and Assay context if a flow cytometric chip data or assay fil

Contents ▲ 462 ▼ IndexHistogram ViewHistograms are graphical representations of the measurement results, where the number of events is mapped to the Y

Contents ▲ 463 ▼ IndexResult TablesThe result tables show a number of calculated values (columns) for each histogram. If you add or redefine markers,

Contents ▲ 464 ▼ IndexNOTEYou can exclude columns from the result tables. Right-click the heading row of the table and select Configure Columns... fro

Contents ▲ 465 ▼ IndexContext MenusIn Single View, two context menus are available.When you right-click a histogram, the following menu appears:The fo

Contents ▲ 466 ▼ IndexWhen you right-click a result table, the following menu appears:The following functions are available:Gate in Blue histogramUses

Contents ▲ 467 ▼ IndexCopy To Clipboard Puts the result table into the clipboard. You can paste the table in another application such as MS Excel®. If

Contents ▲ 468 ▼ IndexDot Plot Tab (Single/Grid View)PurposeDot plots show single events (cells), displayed as dots. In the coordinate system, the red

Contents ▲ 469 ▼ IndexSingle ViewAccessThe Dot Plot tab is always available in the Data and Assay context if a flow cytometric chip data file is selec

Contents ▲ 47 ▼ IndexSwitching Between Electrophoretic and Flow Cytometric AssaysThe Agilent 2100 bioanalyzer supports electrophoretic assays (DNA, RN

Contents ▲ 470 ▼ IndexDot Plot ViewDot plots are graphical representations of the measurement results, where the blue fluorescence intensity is mapped

Contents ▲ 471 ▼ IndexDefault table columns are:NOTEYou can add/exclude columns from the result table. Right-click the table and select Configure Colu

Contents ▲ 472 ▼ IndexContext MenusIn Single View, two context menus are available.When you right-click a dot plot, the following menu appears:The fol

Contents ▲ 473 ▼ IndexWhen you right-click a result table, the following menu appears:The following functions are available:Export... Opens a system d

Contents ▲ 474 ▼ IndexResult Flagging TabPurposeOn this tab, you can define flagging rules for electrophoretic measurement results. A specific color c

Contents ▲ 475 ▼ IndexRule ListLists all user-defined result flagging rules, and the default rule, which you cannot delete. The IF Expression of the d

Contents ▲ 476 ▼ Index• If ExpressionLets you compose an expression from functions, variables, and logical operators.• CommentLets you enter a comment

Contents ▲ 477 ▼ IndexThe following types are used:The following functions are available:Return type DescriptionintInteger number, e.g. 12floatFloatin

Contents ▲ 478 ▼ IndexNOTEPlease refer to the function reference in the Help Pane for details on syntax, usage and examples.TotalAreaReturns the sum o

Contents ▲ 479 ▼ IndexVariablesNOTEPlease refer to the variable reference in the Help Pane for details on syntax, usage and examples.Variable Descript

Contents ▲ 48 ▼ Index• The electrode cartridge contains 16 electrodes that fit into the wells of DNA, RNA, and Protein chips. Each electrode in the ca

Contents ▲ 480 ▼ IndexOperatorsOperators are available for comparison (=, <, <=, >, >=, <>), for arithmetical operations (+, -, *, /

Contents ▲ 481 ▼ IndexLog Book TabPurposeThe Log Book tab shows chip run events in the run log table. For example, you can see when and by whom the ch

Contents ▲ 482 ▼ IndexThe run log table is saved as part of the chip data (.xad) file, and you cannot delete it.Context MenuRight-clicking on the run

Contents ▲ 483 ▼ IndexColumns... Opens a dialog box allowing you to hide, show, and re-sort columns.Column Width... Opens a dialog box allowing you to

Contents ▲ 484 ▼ IndexTabs (Validation Context)In the Validation context the following tabs are available:• Configuration Tab• Results Tab

Contents ▲ 485 ▼ IndexConfiguration TabPurposeThe Configuration tab lets you select qualification tests to be executed in a validation run. During a v

Contents ▲ 486 ▼ IndexButtons:Test PropertiesShows ID, Name and a detailed Description of the qualification test that is selected in the Available Tes

Contents ▲ 487 ▼ IndexResults TabPurposeThe Results tab lets you view detailed results of qualification tests.The results are shown for one test at a

Contents ▲ 488 ▼ IndexTest Name: ...ColumnsButtons:Test PropertiesShows ID, Name, Description, Test Status, and additional information on the selected

Contents ▲ 489 ▼ IndexTabs (Comparison Context)In the Comparison context the following tabs are available:• Comparison Summary Tab• Gel Tab (see “Gel

Contents ▲ 49 ▼ IndexHow to Prepare the Bioanalyzer for Electrophoretic AssaysRemove the pressure cartridge:1 Turn off line power to the Agilent 2100

Contents ▲ 490 ▼ IndexComparison Summary TabPurposeThe Comparison Summary shows information on the selected comparison file, and lets you enter a comm

Contents ▲ 491 ▼ IndexElementsChip icon The chip icon indicates the assay type: DNA, RNA, or Protein.File Name Name of the comparison (.xac) file.Loca

Contents ▲ 492 ▼ IndexIn the Comparison context also the following tabs are available:• Gel Tab (see “Gel Tab” on page 438)• Electropherogram Tab (Sin

Contents ▲ 493 ▼ IndexStatus BarThe status bar at the bottom of the 2100 expert application window shows:• System messages• Progress barA progress bar

Contents ▲ 494 ▼ IndexDialog BoxesThe 2100 expert software provides the following dialog boxes:Dialog Box PurposeGeneral“About 2100 Expert” on page 49

Contents ▲ 495 ▼ Index“Options – Advanced” on page 508 To enable automatic print, automatic export, and automatic chip run.“Page Setup” on page 555 To

Contents ▲ 496 ▼ Index“Configure Marker” on page 545 To configure the marker in a histogram.“Copy Marker” on page 554 To confirm or skip the usage of

Contents ▲ 497 ▼ IndexAbout 2100 ExpertPurposeThis dialog box is used to get information about the installed bioanalyzer hardware and software.AccessY

Contents ▲ 498 ▼ IndexElementsModule/LicenseKeyLists the installed software packages and the associated registration keys that were used to activate t

Contents ▲ 499 ▼ Index2100 Expert – ClosePurposeThis dialog box lets you decide whether or not to save unsaved changes.AccessThis dialog box appears i

Contents ▲ 5 ▼ IndexHow to Use the Advanced Settings ... 299Running I

Contents ▲ 50 ▼ IndexInsert the electrode cartridge:CAUTIONDo not touch the electrodes while the cartridge is in the Agilent 2100 bioanalyzer. The ele

Contents ▲ 500 ▼ IndexElementsSave changes to the following files?If you want to save changes to particular files, you can select or deselect individu

Contents ▲ 501 ▼ IndexOptions – Data FilesPurposeOn the Data Files tab of the Options dialog box, you can specify the names to be used for chip data f

Contents ▲ 502 ▼ IndexElementsYou can make the following settings to specify Data File Names:For example, by including a prefix such as “2100 expert”,

Contents ▲ 503 ▼ IndexYou can specify the directory where you want to store your chip data files (Data File Directory):Default The default directory i

Contents ▲ 504 ▼ IndexOptions – Chip AlertPurposeOn the Chip Alert tab of the Options dialog box, you can specify that the bioanalyzer “beeps” when a

Contents ▲ 505 ▼ IndexElementsOff Turns the alert sound off.Default Sound Standard sound for the chip alert.Custom Sound Allows the use of a custom so

Contents ▲ 506 ▼ IndexOptions – Graph SettingsPurposeYou can compare samples by overlaying their electropherograms/histograms. On the Graph Settings t

Contents ▲ 507 ▼ IndexElementsSignal Color The colored box next to Signal n (where n stands for the sample number) shows the color of the curve in the

Contents ▲ 508 ▼ IndexOptions – AdvancedPurposeOn the Advanced tab of the Options dialog box, you can:• Set disk space limits for data storage• Set au

Contents ▲ 509 ▼ IndexElementsLimit the storage of raw data backupsSelect this option to limit the amount of disk space reserved for raw data storage.

Contents ▲ 51 ▼ Index4 Remove any chip.CAUTIONDo not force the chip selector handle when a chip is inserted in the bioanalyzer. 5 Adjust the chip sele

Contents ▲ 510 ▼ IndexNOTEThe Auto Print and Auto Export settings are independent from the Print... and Export... commands in the File menu (see “File

Contents ▲ 511 ▼ Index2100 expert – End of RunPurposeThis dialog box indicates the end of the current chip run, and any errors associated with the run

Contents ▲ 512 ▼ IndexAborted chip run:ElementsStatus Shows the status of the chip run, either Run Aborted or Run Completed.File Name Name of the data

Contents ▲ 513 ▼ IndexNo. Sample number. A green check next to the sample number indicates a completed measurement, while a white cross on red ground

Contents ▲ 514 ▼ IndexOpenPurposeThis dialog box is used to open• chip data files (.xad), assay files (.xsy), or to import markers or regions from suc

Contents ▲ 515 ▼ IndexAccessYou can open this dialog box by selecting File> Open...ElementsLook in Allows you to select a drive and directory.File

Contents ▲ 516 ▼ IndexExport Options (Flow Cytometry)PurposeThis dialog box is used to export flow cytometric chip data in different formats.AccessYou

Contents ▲ 517 ▼ IndexElementsFlow Cytometry Export categories:Result Tables Creates a .csv file containing result tables. All measured samples are ex

Contents ▲ 518 ▼ IndexExport Directory settings:Buttons:Histogram ImagesExports the histogram images of all samples, two images (red and blue histogra

Contents ▲ 519 ▼ IndexExport Options (Electrophoresis)PurposeThis dialog box is used to export electrophoretic chip data in different formats.

Contents ▲ 52 ▼ IndexHow to Prepare the Bioanalyzer for Flow Cytometric AssaysRemove the electrode cartridge:1 Turn off line power to the Agilent 2100

Contents ▲ 520 ▼ IndexAccessYou can open this dialog box by selecting File > Export ... with an electrophoretic chip data file (.xad) selected.Elem

Contents ▲ 521 ▼ IndexExport Directory settings:Gel Image Exports the gel-like images of all samples. You can export the gel view:• As one image• Each

Contents ▲ 522 ▼ IndexButtons:Custom A target directory of your choice. Use the ... button right to the text field to open the Browse for folder dialo

Contents ▲ 523 ▼ IndexAuto ExportPurposeTo set options for automatic export, which takes place each time a chip run is complete.AccessYou can open thi

Contents ▲ 524 ▼ IndexResult Tables Creates a CSV file (.csv) containing result tables. All measured samples are exported to one file.Sample Data Expo

Contents ▲ 525 ▼ IndexElectrophoresis Data Export tabResult Tables Creates a CSV file (.csv) containing result tables. All measured samples are export

Contents ▲ 526 ▼ IndexSample Data Exports text list files (.csv), one file per sample. These files are intended for advanced users who want to closely

Contents ▲ 527 ▼ IndexDefault Export Directories tabExport Directories It is advisable to specify individual target directories for Result Tables, Sam

Contents ▲ 528 ▼ IndexPrint (Flow Cytometry)PurposeThis dialog box is used to set print options for flow cytometric chip data and assay files and to s

Contents ▲ 529 ▼ IndexElementsPrint ItemRun Summary Includes chip and sample information in the printout. See “Chip Summary Tab” on page 427.Assay Det

Contents ▲ 53 ▼ IndexCAUTIONStore the electrode cartridge in the provided box. If the pins of the electrode cartridge are bent or misaligned, poor qua

Contents ▲ 530 ▼ IndexSave To FilePDF Redirects the printout to a .pdf file. Clicking on the ... button opens a system dialog box allowing you to spec

Contents ▲ 531 ▼ IndexPrint (Electrophoresis)PurposeThis dialog box is used to set print options for electrophoretic chip data or assay files and to s

Contents ▲ 532 ▼ IndexElementsPrint ItemRun Summary Includes chip and sample information in the printout. See “Chip Summary Tab” on page 427.Assay Det

Contents ▲ 533 ▼ IndexOptions Select how many electropherograms to print per page. Affects the printout only if Electropherogram is selected under Pri

Contents ▲ 534 ▼ IndexCancel Exits the dialog box without printing.Print/Save If you selected any option under Save To File, the button is labeled Sav

Contents ▲ 535 ▼ IndexPrint (Validation)PurposeThis dialog box is used to set print options for validation reports and to start printing.AccessYou can

Contents ▲ 536 ▼ IndexElementsPrint ItemIQ SW Includes the results of all installation qualification tests for the 2100 expert system software.IQ HW I

Contents ▲ 537 ▼ IndexPrinter... Opens the Print Setup dialog box, allowing you to select a printer, and set the page size and page orientation.Previe

Contents ▲ 538 ▼ IndexPrint (Comparison)PurposeThis dialog box is used to set print options for comparison reports and to start printing.AccessYou can

Contents ▲ 539 ▼ IndexElementsPrint ItemComparison SummaryIncludes information on the comparison file in the printout.Assay Details Includes assay nam

Contents ▲ 54 ▼ Index4 Remove any chip.CAUTIONDo not force the chip selector handle when a chip is inserted in the bioanalyzer. 5 Adjust the chip sele

Contents ▲ 540 ▼ IndexSave To FilePDF Redirects the printout to a .pdf file. Clicking on the ... button opens a system dialog box allowing you to spec

Contents ▲ 541 ▼ IndexAuto PrintPurposeTo set options for automatic printouts, that are to be generated each time a chip run is complete.AccessYou can

Contents ▲ 542 ▼ IndexElementsPrint ItemAssay Details Includes assay name, path, and setpoints in the printout. See “Assay Properties Tab” on page 418

Contents ▲ 543 ▼ IndexConfigure ColumnsPurposeThis dialog box is used to show or hide columns of tables.AccessYou can display this dialog box by openi

Contents ▲ 544 ▼ IndexElementsAvailable This list on the left shows you all available but currently not displayed columns.Displayed This list on the r

Contents ▲ 545 ▼ IndexConfigure MarkerPurposeThis dialog box is used to set the properties of the selected marker in a histogram.AccessYou can open th

Contents ▲ 546 ▼ IndexElementsName Enter a name for the marker. Easy-to-remember names, for example the used dye, make it easier to identify the marke

Contents ▲ 547 ▼ IndexConfigure RegionPurposeThis dialog box is used to set the properties of the selected region in a dot plot.AccessYou can open thi

Contents ▲ 548 ▼ IndexTop, Bottom, Left, RightThe four values define a rectangular region. You can change the size of the region by entering different

Contents ▲ 549 ▼ IndexInsert Existing MarkersPurposeThis dialog box is used to add existing markers to histograms.AccessWhen a histogram is displayed

Contents ▲ 55 ▼ IndexRunning and Evaluating Electrophoretic AssaysFor running and evaluating electrophoretic assays you need to know the following:• “

Contents ▲ 550 ▼ IndexElementsIf you change the properties of a marker, the properties will change accordingly in all other histograms that use this m

Contents ▲ 551 ▼ IndexInsert Existing RegionPurposeThis dialog box is used to add an existing region to a dot plot.AccessWhen a dot plot is displayed

Contents ▲ 552 ▼ IndexDescriptionAll existing regions are listed except the ones that are already used by the current dot plot. If you change the prop

Contents ▲ 553 ▼ IndexCopy RegionPurposeTo confirm or skip the usage of the currently selected region as a reference region for all samples.AccessThe

Contents ▲ 554 ▼ IndexCopy MarkerPurposeTo confirm or skip the usage of the currently selected marker as a reference marker for all samples.AccessThe

Contents ▲ 555 ▼ IndexPage SetupPurposeThis dialog box lets you change the layout of the printed page.ElementsSize Allows you to select the paper form

Contents ▲ 556 ▼ IndexPortrait Prints data in portrait orientation.Landscape Prints data in landscape orientation.Margins Defines the borders of the

Contents ▲ 557 ▼ IndexReport PreviewPurposeThis window is used to display a preview of all pages that will be printed.AccessYou can open this window b

Contents ▲ 558 ▼ IndexElementsYou can browse through the print preview and modify the display using the functions in the toolbar:Table of Contents Dis

Contents ▲ 559 ▼ IndexSave Selected Samples ...PurposeThis dialog box is used to select a subset of the current .xad file’s samples for saving.AccessI

Contents ▲ 56 ▼ IndexPrinciples of Nucleic Acid and Protein Analysis on a ChipThe electrophoretic assays are based on traditional gel electrophoresis

Contents ▲ 560 ▼ IndexElementsData File Name of the chip data (.xad) file you selected for selective saving.Location Path to the Data File.ID Sample n

Contents ▲ 561 ▼ IndexSystem Log ViewerPurposeThe system log table shows system-wide events. For example, you can see who started the 2100 expert soft

Contents ▲ 562 ▼ IndexAccessYou can open this dialog box by selecting System Log from the Tools menu.System Log TableThe system log table has the foll

Contents ▲ 563 ▼ IndexContext MenuRight-clicking on the system log table opens a context menu:Hide Column Hides the selected column.Show All ColumnsSh

Contents ▲ 564 ▼ IndexToolbarThe System Log Viewer window provides a toolbar that works in the same way as the Log Book toolbar, see “Data and Assay C

Contents ▲ 565 ▼ IndexShortcuts and Mouse ActionsYou can enter data and commands either by using the keyboard or the mouse.• Shortcuts can be used to

Contents ▲ 566 ▼ IndexAlt ShortcutsPress and hold down the Alt key while pressing another key:Function KeysThese are the function keys located at the

Contents ▲ 567 ▼ IndexArrow KeysThe arrow keys are located to the left of the numerical key pad on your keyboard.Shortcut Function→ Moves the input fo

Contents ▲ 568 ▼ IndexMouse ActionsThe mouse lets you make efficient use of 2100 expert’s graphical user interface. Left-click ResultIn Toolbars Activ

Contents ▲ 569 ▼ IndexIn Single View Histograms: selects a marker.Dot plots: selects a region.At the right edge of the window on electropherograms and

Contents ▲ 57 ▼ IndexRNA are electrophoretically driven by a voltage gradient—similar to slab gel electrophoresis. Because of a constant mass-to-charg

Contents ▲ 570 ▼ IndexDouble left-click ResultIn Single View On markers in histograms: opens the Configure Marker dialog box.On region borders in dot

Contents ▲ 571 ▼ IndexRight-click ResultIn Tree View Panel Data and Assay context: selects a file or sample, and opens a context menu allowing you to

Contents ▲ 572 ▼ IndexDrag ResultIn Single View Zooms into the graph. In electropherograms, also pan and scale operations are possible.Histograms: The

Contents ▲ 573 ▼ IndexProducts, Spare Parts, and AccessoriesTo buy the following products, spare parts and accessories for the Agilent 2100 bioanalyze

Contents ▲ 574 ▼ Index• G2947CA – Agilent 2100 bioanalyzer electrophoresis setIncludes test chip kit, electrode cartridge, license key for electrophor

Contents ▲ 575 ▼ Index• G2938-81605 – RS 232 cableCommunication cable PC – instrument• 2110-0007 – FuseTwo power supply fuses are needed for the G2938

Contents ▲ 576 ▼ IndexGlossaryThis glossary explains terms in context with flow cytometry, electrophoresis, and software or hardware of the Agilent 21

Contents ▲ 577 ▼ IndexThe figure below shows baselines established for DNA assay peaks. Peaks for DNA and protein assays are determined on a peak-by-p

Contents ▲ 578 ▼ IndexThe figure below shows baselines established for Total RNA assay fragments. Total RNA fragments are determined on a peak-by-peak

Contents ▲ 579 ▼ IndexThe figure below shows baselines established for an mRNA assay. mRNA fragments are determined on a peak-by-peak basis and an ove

Contents ▲ 58 ▼ IndexThe 2100 expert software plots fluorescence intensity versus migration time and produces an electropherogram for each sample:

Contents ▲ 580 ▼ IndexNOTEWith RNA assays, you can move the lines marking the start and end points for data analysis (shown by the long-dashed vertica

Contents ▲ 581 ▼ IndexCCAD fileIn Cell Fluorescence flow cytometric chip runs were stored as .cad files. 2100 expert can import .cad files. See also X

Contents ▲ 582 ▼ IndexDData FilteringThe first step 2100 expert takes in analyzing raw data is to apply data filtering. Data filtering is done by mean

Contents ▲ 583 ▼ IndexElectrokinetic forcesElectrokinetic forces are used to move, switch and separate the samples. Active control over voltage gradie

Contents ▲ 584 ▼ IndexEnd PointThe peak find algorithm looks for a leveling off when the value of the slope is less than the value set for the slope t

Contents ▲ 585 ▼ IndexFirmwareThe firmware is a program to control the hardware of the Agilent 2100 bioanalyzer. It is downloaded from your computer t

Contents ▲ 586 ▼ IndexHTML fileHTML (Hyper Text Markup Language) is the authoring language used to create documents on the World Wide Web. HTML define

Contents ▲ 587 ▼ IndexLab-on-a-chip technology means downsizing of analytical techniques from lab-scale to chip-scale:• using techniques like electrop

Contents ▲ 588 ▼ IndexMMicrofluidicsThe movement of liquids through micro-fabricated structures by means of electrical fields or pressure/vacuum, hold

Contents ▲ 589 ▼ IndexMiniaturized laboratories on a microchipExpression used to describe lab-on-a-chip technology.Minimum Peak HeightThe Minimum Peak

Contents ▲ 59 ▼ IndexThe data can also be displayed as a densitometry plot, creating a gel-like image:

Contents ▲ 590 ▼ IndexPDF filePDF (Portable Document Format) is a file format created by Adobe Systems Incorporated that preserves all of the fonts, f

Contents ▲ 591 ▼ IndexPeak HeightThe value at the center point of the peak minus the local baseline start value.Point-to-Point FitThis curve fit is co

Contents ▲ 592 ▼ IndexPriming StationConsists of a chip holder that has a syringe mounted on the lid that seals over the chip. The syringe is used to

Contents ▲ 593 ▼ IndexRRaw data backup fileSee PCK file.SSerial portThe serial ports (COM ports) are used to connect your computer with the Agilent 21

Contents ▲ 594 ▼ IndexStart TimeThis setting determines the time after which the first peak or fragment will be located (any peaks appearing before th

Contents ▲ 595 ▼ IndexUUpper MarkerAn internal standard that is added to a DNA or Protein sample in a well to assist in determining size and concentra

Contents ▲ 596 ▼ IndexXLS fileMicrosoft Excel spreadsheet file.XML fileExtensible Markup Language files. XML is the Extensible Markup Language, a syst

Contents ▲ 597 ▼ IndexZZero BaselineAll electropherograms produced with the bioanalyzer show some amount of background fluorescence. By default, the 2

Contents ▲ 598 ▼ IndexTo remove the zeroing, disable the Zero Baseline box in the setpoint explorer (baseline calculation under Global and Advanced se

Contents ▲ 599 ▼IndexAAccessories, 573Adding regions, 221Agilent Online Store, 573Alert sound, 296Antibody staining, 230APC, 159Apoptosis assays, 235A

Contents ▲ 6 ▼ IndexAbout this ManualWelcome to the User’s Guide for the Agilent 2100 expert software. This manual provides beginners and advanced use

Contents ▲ 60 ▼ IndexPreparing and Running an Electrophoretic AssayAn electrophoretic chip run requires the following steps:1. Set up and switch on th

Contents ▲ 600 ▼ IndexDDataspecify file names and directories, 294Data analysis setpoints, 111data analysis setpoints, 249Data files, 247Data points,

Contents ▲ 601 ▼ IndexLogRun log, 287System Log, 287MManual integration, 124Marker, 200configuring, 209copying, 212inserting, 207limits, 211removing,

Contents ▲ 602 ▼ IndexSScaleoverlaid histograms, 216Setpoint Explorer, 425Setpoints, 249Show data points, 88, 197Sieving polymer, 56Single channel mod

Contents ▲ 61 ▼ Index• Analyze and evaluate the results:– “Analyzing and Evaluating the Results of an Electrophoretic Assay” on page 91– “Result Flagg

Contents ▲ 62 ▼ IndexSelecting an Electrophoretic Assay for a Chip RunTo select an assay:1 Switch to the Instrument context.2 In the Tree View Panel,

Contents ▲ 63 ▼ Index3 If you do not see one of these icons, check that the bioanalyzer is switched on and properly connected:– Check the COM port set

Contents ▲ 64 ▼ IndexBoth will open the Assays menu, allowing you to select an assay from the submenus.– OR – Select File > Open File to Run... Th

Contents ▲ 65 ▼ IndexNOTEAfter a chip run, the results can be evaluated using a different electrophoretic chip data file (.xad) of the same assay type

Contents ▲ 66 ▼ IndexPreparing Samples and Chips for Electrophoretic AssaysBefore you can fill a chip, you have to prepare the samples. To find out ho

Contents ▲ 67 ▼ IndexEssential Measurement Practices (Electrophoretic Assays)General:WARNINGWear hand and eye protection and follow good laboratory pr

Contents ▲ 68 ▼ Index• Protect dye and gel-dye mix from light. Remove light covers only when pipetting. Dye decomposes when exposed to light.• Use a n

Contents ▲ 69 ▼ IndexProtein Assays:• Store Protein sample buffer at -20 °C upon arrival. Keep the vial in use at 4 °C to avoid freeze-thaw cycles.• A

Contents ▲ 7 ▼ IndexIn this ManualThis manual provides bioanalyzer users with the following information:• “About this Manual” on page 6 gives an overv

Contents ▲ 70 ▼ IndexLoading the Electrophoresis Chip into the BioanalyzerAfter preparing the chip, you can insert it into the Agilent 2100 bioanalyze

Contents ▲ 71 ▼ Index3 Carefully close the lid. CAUTIONDo not force the lid closed. This may damage the cartridge. If the lid does not close completel

Contents ▲ 72 ▼ IndexRunning an Electrophoretic AssayRunning an electrophoretic assay in 2100 expert just means pressing a button.NOTEYou can stop a c

Contents ▲ 73 ▼ IndexThe number of the sample that is currently being measured is indicated on the information bar:

Contents ▲ 74 ▼ IndexThe status bar shows the name of the currently measured sample, a progress bar showing the measurement progress for the current s

Contents ▲ 75 ▼ IndexFinishing the Chip RunWhen the measurements are finished, the End of run dialog box appears, showing you the number of samples th

Contents ▲ 76 ▼ IndexThe dialog box is closed.• If you selected Select file in Data Context, you are automatically taken to the Data and Assay context

Contents ▲ 77 ▼ IndexStopping a Chip RunYou can stop a chip run at any time, for example, • if the quality of the measurement results does not meet yo

Contents ▲ 78 ▼ IndexThe following message appears:2 Click Yes to stop the chip run.The End of Run dialog box appears.

Contents ▲ 79 ▼ IndexThe measured samples are marked with a green check, and only these are stored in the chip data file.The unmeasured samples are ma

Contents ▲ 8 ▼ Index• “Configuring 2100 Expert” on page 293 is your guideline for configuring the 2100 expert software.• “Running Instrument Diagnosti

Contents ▲ 80 ▼ IndexEntering Chip, Sample, and Study InformationDuring or after a chip run, you can document the run by entering information on chip,

Contents ▲ 81 ▼ IndexNOTEYou may find some input fields already filled in, because chip, sample, and study information are taken over from the base as

Contents ▲ 82 ▼ IndexDisplaying the Measurement Results (Electrophoresis)You can view the measurement results of an electrophoretic chip run as electr

Contents ▲ 83 ▼ IndexHow to Switch Between Single View and Grid View (Electropherograms)To switch between single view and grid view:1 From the Electro

Contents ▲ 84 ▼ IndexHow to Navigate Through the SamplesAt any time—even during a chip run—you can scroll through all samples—either in electropherogr

Contents ▲ 85 ▼ IndexTo browse through samples:1 From the Electropherogram or Gel menu, select Next Sample or Previous Sample.– OR –Click the Next Sam

Contents ▲ 86 ▼ IndexTo zoom into an electropherogram:1 From the Electropherogram menu, select Graph Mode > Zoom (default setting). 2 Position the

Contents ▲ 87 ▼ IndexTo pan and scale an electropherogram:1 From the Electropherogram menu, select Graph Mode > Pan or Scale. 2 Position the mouse

Contents ▲ 88 ▼ IndexTo display data points in an electropherogram:1 From the Electropherogram menu, select Show Data Points or click the button in

Contents ▲ 89 ▼ IndexCleaning the Electrodes after an Electrophoretic AssayWhen the assay is complete, remove the used chip from the bioanalyzer and d

Contents ▲ 9 ▼ IndexRelated DocumentsA collection of supplemental literature is given in the following. Bioanalyzer ManualsCD-ROMReagent Kit GuidesThe

Contents ▲ 90 ▼ IndexCAUTIONNever use a cloth to clean the electrodes. Electrostatic discharge could damage the high-voltage power supplies.CAUTIONWet

Contents ▲ 91 ▼ IndexAnalyzing and Evaluating the Results of an Electrophoretic AssayThe purpose of electrophoretic assays is to calculate the size an

Contents ▲ 92 ▼ IndexData Analysis: DNAThe data analysis process for DNA assays consists of the following steps:1. Raw data is read and stored by the

Contents ▲ 93 ▼ Index4. A sizing ladder (see the example electropherogram below), which is a mixture of DNA fragments of known sizes, is run first fro

Contents ▲ 94 ▼ Index5. A standard curve of migration time versus DNA size is plotted from the DNA sizing ladder by interpolation between the individu

Contents ▲ 95 ▼ Index6. Two DNA fragments are run with each of the samples, bracketing the DNA sizing range. The “lower marker” and “upper marker” are

Contents ▲ 96 ▼ Index8. To calculate the concentration of the individual DNA fragments in all sample wells, the upper marker, in conjunction with an a

Contents ▲ 97 ▼ IndexData Analysis: RNA and Cy5-Labeled Nucleic AcidsThe data analysis process for RNA and the Cy5-labeled nucleic acids assays consis

Contents ▲ 98 ▼ IndexNOTEPeak ratios for the RNA ladder may vary from one batch of RNA 6000 ladder to the next. Assay performance will not be affected

Contents ▲ 99 ▼ IndexRNA AssaysThe marker solution that is part of each RNA LabChip kit, contains a 50 bp DNA fragment. This fragment is used as lower