Experion DNA 1K & 12K Analysis Kits

8/14/2019 Experion DNA 1K & 12K Analysis Kits

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Experion DNA

1K Analysis KitInstruction Manual

For Technical Service call your local Bio-Rad office or in the US Call 1-800-4BIORAD (1-800-424-6723)


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Table of Contents

Section 1 Introduction ...........................................................11.1 Background Information ..................................................11.2 Product Description.........................................................31.3 Specifications ..................................................................51.4 Additional Equipment Required But Not Included ..........51.5 Storage Conditions..........................................................6

Section 2 Procedure ..............................................................7Please read through procedure in its entirety prior to beginning experiments.

2.1 Procedure Overview........................................................72.2 Essential Practices..........................................................82.3 Turning on Experion Electrophoresis Station and

Launching Experion Software .......................................102.4 Equilibrating Kit Reagents to Room Temperature.........112.5 Preparing the Gel-Stain ................................................112.6 Preparing the Samples and DNA 1K Ladder................132.7 Priming the Chip ...........................................................142.8 Loading the Samples and DNA 1K Ladder

into the Chip..................................................................17


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2.9 Running the DNA 1K Analysis......................................192.10 Cleaning the Electrodes After a Run ............................20

Section 3 Data Analysis ......................................................213.1 Example of a DNA 1K Ladder Separation ....................213.2 Example of a DNA Sample Separation.........................23

Section 4 Troubleshooting..................................................254.1 Electrophoresis, Vortex, and Priming Stations..............25

4.2 DNA 1K Analysis...........................................................26Section 5 Ordering Information ..........................................33

Section 6 Legal Notices ......................................................36

Section 7 Appendix..............................................................377.1 How to Clean the Electrodes ........................................377.2 Quick Start Instructions.................................................39


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Section 1Introduction

1.1 Background Information

LabChip microfluidic technology provides new opportunities in thedevelopment of proteomic and genomic expression analyses. The Experionautomated electrophoresis system (Figure 1.1) employs LabChip microfluidictechnology to automate electrophoresis for protein, RNA, and DNA analysis.This microfluidics-based system integrates separation, detection, and dataanalysis within a single platform. Refer to Bulletin 5285 for additionalinformation on how the Experion system employs this technology.

At the center of the Experion system is the microfluidic chip, whichcontains a series of plastic wells bonded over a small glass plate. The

glass plate is etched with an optimized network of microchannels, one ofwhich intersects with each of the plastic wells. Once these channels havebeen primed with a gel matrix and the samples applied to the appropriatewells, the electrophoresis station directs the samples through thesemicrochannels by precisely controlling the voltages and currents that areapplied. The microfluidic chip, along with the Experion reagents,electrophoresis station, and software, (Figure 1.1) are designed to

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accomplish several sequential procedures, including separation, staining,detection, and basic data analysis without any user intervention.

Fig. 1.1. The Experion system includes the following components: (1) Automated

electrophoresis station, (2) Priming station, (3) Vortex station for RNA and DNA analysis, (4)

System operation and data analysis tools, and (5) Analysis kits, which include the (a) chips

and (b) reagents for protein (Pro260 kit), standard-sensitivity RNA (StdSens kit), high-sensitivity

RNA (HighSens kit), and DNA (1K and 12K kits) analysis.

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5a

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1.2 Product Description

Each Experion analysis kit contains the chips and reagents required to

perform DNA electrophoresis in the range between 25 and 1,000 basepairs (bp). The kits are available in a 10-chip configuration. The ExperionDNA 1K analysis kit offers single-step determination of DNA size, purityand concentration at nanogram levels. High-resolution separation andaccurate sizing and quantitation of DNA samples are achieved through thecombination of chip design innovations and a very accurate DNA ladder,

which is included in the kit. The DNA 1K analysis kit uses lower (15 bp)and upper (1,500 bp) internal markers for alignment. The DNA 1K kit cananalyze 111 DNA samples in approximately 40 minutes.

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DNA 1K Kit Reagents

Item Description Volume/Vial 10-Chip Kit

DNA 1K gel Proprietary 250 l 3 vialspolymer sieving matrix

DNA stain Proprietary 40 l 1 vialfluorescent dye

DNA 1K loading Contains lower 750 l 1 vial

buffer and upper alignmentmarker

DNA 1K ladder 11 distinct DNA 20 l 1 vialfragments of 25to 1,000 bps

Spin filters N/A 3 each

DNA 1K Chips

Item 10-Chip Kit

DNA chip 10 chips

Cleaning chip 1 chip

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1.3 Specifications

Specification Kit

Number of wells 11Sample volume 1 l

Total run time ~40 min

Quantitative range (total DNA concentration) 0.150 ng/l

Maximum salt concentration of sample 200 mM KCl or NaCl, 15 mM MgCl2

1.4 Additional Equipment Required but Not Included

Experion electrophoresis station

Experion priming station

Experion vortex station

Calibrated pipets (p10, p20, p200, p1000). A p10 micropipet isrecommended for dispensing the gel, loading buffer, ladder andsamples onto the chip

0.65 ml DNase-free microcentrifuge tubes for sample dilution (if

needed) and for preparing 65 l aliquot of loading buffer

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DNase-free pipet tips as needed. It is recommended that a new tipbe used for each delivery

Aluminum foil to cover and protect DNA stain and gel-stain mixfrom light

Microcentrifuge

Vortexer

Water, DNase-free, 0.2 m filtered (Experion DEPC-treated water,catalog #700-7253 is recommended)

Experion electrode cleaner (catalog #700-7252)

Ice bucket with ice

1.5 Storage ConditionsItem Storage Conditions

Experion DNA 1K reagents 4C

Experion DNA 1K chips Ambient

Filtered gel-stain (see Section 2.5) 4C

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Section 2Procedure

2.1 Procedure Overview

This is a multistep procedure. It is necessary to thoroughly read andunderstand each step prior to performing chip separations.

1. Turn on Experion electrophoresis station and launch Experion software.

2. Equilibrate kit reagents to room temperature.

3. Prepare gel-stain.

4. Prepare samples and DNA 1K ladder.

5. Prime chip with gel-stain solution.

6. Load samples and DNA 1K ladder into chip and vortex chip.

7. Run DNA 1K analysis.

8. Clean instrument electrodes.

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2.2 Essential Practices

Store all reagents at 4C when not in use

Always protect the DNA stain and gel-stain solution (see Section 2.5)from light! Components in these reagents are light sensitive

Before using, allow all kit reagents to equilibrate to roomtemperature (~1520 minutes). The DNA stain contains DMSO andshould be completely thawed before use

Vortex and briefly centrifuge all kit reagents before use

Use DNase-free microcentrifuge tubes, pipet tips, and TE buffer asneeded

Avoid sources of dust or other contaminants when preparing samples

and loading the chip. Foreign particles in reagents, samples, or inthe wells of the chip will block microchannels and interfere withresults

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Always wear powder-free gloves when handling the reagents andchips. Handle chips by their edges and do not touch the glass assmudges and fingerprints could interfere with detection. The chipsshould only be removed from their packaging immediately prior touse to avoid introduction of any particulates from the air into thewells

Run a loaded chip within 5 minutes. Otherwise, excessiveevaporation may occur, leading to poor results or a chip performance

error

Do not open the electrophoresis station while running an analysis

Never place the electrophoresis station on or near a vibratingsurface as laser focusing could be affected

Dispense reagents into chips slowly. Always insert the pipet tipcentered, vertically, and to the bottom of the chip well whendispensing liquids. Do not expel air at the end of the pipetting step;dispense to the first stop of the pipet. This method of pipetting willreduce the possibility of air bubbles becoming trapped between thereagent and the opening to the microchannel at the bottom of the

chip wells

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Always follow the recommended electrode cleaning procedure toavoid contamination

Coated or treated tubes (for example, siliconized polypropylene)should not be used in the preparation of the kit reagents or samples.Use of treated tubes may lead to poor results due to artifacts duringthe separation

2.3 Turning on Experion Electrophoresis Station andLaunching Experion Software

1. Turn on the power to the Experion electrophoresis station by pushingthe green button in the center of the front panel. The steady green LEDabove the button indicates that the unit is on.

2. Launch the Experion software application.

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2.4 Equilibrating Kit Reagents to Room Temperature

1. Remove the DNA stain (blue cap), DNA loading buffer (yellow cap),

and 1 tube of DNA 1K gel (green cap) from storage and equilibrate toroom temperature for ~1520 minutes. Keep the stain covered at alltimes to avoid exposure to light by wrapping the tube in aluminum

foil.

Note: If filtered gel-stain was previously prepared, remove it from

storage and equilibrate as detailed above.2. Invert each tube several times and then vortex the contents of each

tube to reincorporate any condensed liquid formed upon storage. Brieflycentrifuge each tube to bring the solutions to the bottom of the tubes.Make sure the DMSO in the stain is completely thawed beforeproceeding.

2.5 Preparing the Gel-Stain

Note: Skip this section if filtered gel-stain is already available.

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1. Add exactly 12.5 l DNA stain (blue cap) to a tube of 250 l DNA 1KGel (green cap). Vortex the contents thoroughly for 10 seconds, andthen briefly centrifuge to collect the solution at the bottom of the tube.

2. Transfer all of the gel-stain solution (GS) to a spin filter tube. Label anddate the tube.

3. Centrifuge the spin filter tube containing the gel-stain at 2,400 x g for15 minutes.

4. Visually inspect the spin filter to ensure that all of the gel-stain haspassed through the filter, continuing centrifugation if necessary, andthen discard the filter basket. Blue staining of the filter membrane isnormal. Wrap the tube of gel-stain in aluminum foil to protect the stainfrom light.

Notes:

Use the filtered gel-stain within 4 weeks of preparation. After 4weeks, discard the solution. The filtered gel-stain should NOT berefiltered and used

Keep the gel-stain protected from light and store at 4C when not in

use

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Each tube of filtered gel-stain should contain sufficient solution forat least 5 chips

5. Cap the tube of DNA stain tightly, since DMSO is hygroscopic. Store itin the dark at 4C.

2.6 Preparing the Samples and DNA 1K Ladder

1. DNA Ladder: Remove the DNA 1K ladder (clear cap) from storage,

briefly centrifuge, and then vortex to mix. Place the tube of ladder onice.

2. DNA samples: Important considerations.

The total DNA sample concentration must be within the linearrange of the assay (0.150 ng/l); make an appropriate dilution of

the sample, for example in 10 mM Tris, 1 mM EDTA (pH 8) buffer(TE buffer), as needed

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The concentration of salt in the DNA sample must be less than200 mM KCl or NaCl, 15 mM MgCl2. Higher solution conductivityreduces the amount of sample injected onto the chip, affectingassay sensitivity and potentially reducing quantitation accuracy andprecision. Make an appropriate dilution of the sample, for examplein TE buffer, as needed

Restriction enzyme digests may require the addition of EDTA tochelate metal ions, and/or heat inactivation of the enzyme prior to

running the chip. Failure to inactivate the restriction enzyme mayresult in degradation of the internal DNA markers, inaccurate siz-ing, and/or peak broadening

2.7 Priming the Chip

1. Open the Experion priming station by pressing down on the front lever.

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2. Remove an Experion DNA 1K chip from itspackaging and place it on the chip platform,matching the arrow on the chip with thealignment arrow on the chip platform. A poston the chip prevents insertion in the wrongposition. Do not force the chip into position.

3. Pipet 9 l filtered gel-stain solution (fromSection 2.5) into the highlighted well labeled

GS (gel priming well). Insert the tip of the pipet vertically, centered andto the bottom of the well when dispensing. Do not expel air at the end ofthe pipetting step.

Warning: Placing the pipet tip at the edge of the well or allowing the gelto slide down the wall of the well may lead to bubble formation at the

bottom of the well. It is acceptable if 12 small bubbles form at the sur-face. Dislodge bubbles at the bottom with a clean pipet tip, or removethe gel-stain and refill the well.

4. Carefully close the priming station by gently pressing down on lid. Thelid should snap completely closed.

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Gel primingwell

Alphanumericpriming code


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5. Set the pressure setting to C and the time setting to 3, as specified bythe alphanumeric code on the chip. The selected option on the primingstation has the letter or number in bold with clear backing.

6. Press the Start button. The Priming message will illuminate on theLCD screen, the priming station will pressurize, and the timer will countdown. Complete priming requires approximately 60 seconds. Do notopen the priming station during the countdown.

7. An audible signal indicates that priming is complete, and a Readymessage will be displayed. Open the priming station by pressing downon the release lever.

8. Turn the chip over and inspect the microchannels for bubbles or evi-dence of incomplete priming. The microchannels will appear opaqueand will be difficult to see if the chip is primed properly. If you detect a

problem, such as a bubble or incomplete priming, prime a new chip.

Note: Do not touch the glass surface of the chip. Always handle thechips by the sides.

9. Place the chip on a clean surface for loading samples.

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2.8 Loading the Samples and DNA 1K Ladder Intothe Chip

1. Pipet 9 l of the gel-stain solution into the other 3wells labeled GS.

2. Pipet 5 l of the loading buffer (yellow cap) in eachsample well (111) and the ladder well, labeled L.

Use a new pipet tip for each delivery to prevent

contamination of the loading buffer stock.Alternatively, remove 65 l of loading buffer into aDNase-free microcentrifuge tube and pipet 5 l toeach well from this volume

Make sure the pipet tip is centered and positioned vertically all the

way to the bottom of the well. Avoid introducing bubbles into thebottom of the wells. One method is to dispense only to the first stopon the pipetr. It is acceptable if 12 small bubbles form at thesurface

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All wells should be filled with the loading buffer, even when fewerthan 11 samples are run. The chip will not run properly unless allwells are filled

3. Inspect the wells to make sure that there is no excessive bubbleformation from pipetting. This can be done by holding the chip above alight-colored background and looking down through the wells.

4. Pipet 1 l DNA 1K ladder into the well labeled L.

Every chip must have the DNA 1K ladder loaded into the ladderwell for accurate quantitation of samples and for sample alignment

5. Pipet 1 l sample into each of the 11 sample wells.

6. If running fewer than 11 samples, add 1 l loading buffer, TE buffer, orDNase-free water to the unused sample well(s).

7. Place the chip in the Experion vortex station, making sure it is securelyclipped into position.

8. Turn on the vortexer, which will operate for 60 seconds and thenautomatically shut off. Remove the chip when the vortexer stops andtoggle the switch to silence the audible alarm.

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9. Once again, briefly inspect the wells to confirm that there is noexcessive bubble formation from pipetting, and that no liquid has spiltoutside the wells during the vortexing step.

10. Start the run immediately (within 5 minutes) to prevent excessiveevaporation and poor results or a chip performance error.

2.9 Running the DNA 1K Analysis

1. Open the lid of the electrophoresis station. Place the primed chip,which has been loaded with samples, onto the chip platform. Ensurethat the chip is seated properly and then carefully close the lid.

2. Select New Run. Select the DNA 1K protocol from the dropdownmenu.

3. Enter or select a project name and then enter a run name prefix. Clickon the Start icon . In the ensuing popup window, enter the numberof samples to be run (default is all 11 samples are to be analyzed)and/or press the Start button to begin the chip run.

4. After a run has started, the green LED in the center of the front panelof the electrophoresis station will begin blinking indicating that a run isin progress.

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5. When the chip run is complete, a Run complete message will bedisplayed. Press the OK button, remove the chip from the electrophoresisstation and dispose of it properly. To prevent contamination of the

electrodes, do not leave the chip in the electrophoresis station for anextended period of time. It is good practice to insert the cleaning chipwith water and close the lid (see Section 2.10) as soon as the DNAchip is removed. This will help prevent samples and/or buffers fromdrying on the electrodes.

2.10 Cleaning the Electrodes After a Run

1. Fill the cleaning chip with 800 l DNase-free water. Gently tap the sideof the cleaning chip to remove any trapped bubbles from the wells.

2. Open the lid of the electrophoresis station and place the cleaning chip

onto the chip platform.3. Close the lid and leave it closed for about 60 seconds.

4. Open the lid and remove the cleaning chip.

5. Allow the electrodes to dry for 60 seconds.

6. Close the lid.

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7. Replace the water in the cleaning chip after each use to avoid contami-nation. For storage, remove the water from the cleaning chip and storethe chip in a clean location.

Section 3Data Analysis

Examples of electropherograms generated by the Experion software

are provided in this section. For detailed instructions on using the softwareanalysis tools, refer to the software help.

3.1 Example of a DNA 1K Ladder Separation

At the end of each run, the Experion software will display anelectropherogram of the DNA 1K ladder run in the ladder (L) well of theDNA 1K chip. Separation of the DNA 1K ladder generates 13 peaks in theelectropherogram (Figure 3.1). The software will identify the first peak asthe lower alignment marker and the last peak as the upper alignmentmarker. If the DNA separation was successful, all the DNA peaks in theladder should be well resolved.

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Fig. 3.1. Electropherogram of the Experion DNA 1K ladder illustrating relative positions

of the lower 15 bp marker, upper 1,500 bp marker, and 11 DNA peaks ranging in size

from 25 bp to 1,000 bp.

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3.2 Example of a DNA Sample Separation

Figure 3.2 shows an electropherogram of a commercial preparation of

pBR322 DNA plasmid (25 ng/l) digested with the restriction enzymeBsuRI (HaeIII) and separated with the Experion DNA 1K analysis kit. Thefirst and last peak in the electropherogram correspond to the 15 bp lowermarker and the 1,500 bp upper marker, respectively. The two markers arepresent in the Experion DNA 1K loading buffer and are used for alignmentof the sample lanes to the ladder. Additionally, the upper marker is used in

calculations of DNA peak quantity. Of the 22 expected fragments, 18 aredetected. Two fragments, 124 bp and 123 bp, are not resolved and migrateas a single peak; the software assists in the recognition of such overlappingpeaks in restriction digests by reporting peak molarity as well asconcentration. Four small fragments, ranging in size from 8 to 21 bp, arenot visible in the electropherogram due to their concentration being below

the limit of detection.

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Fig. 3.2. Electropherogram of a BsuRI (HaeIII) digest of a pBR322 plasmid sample. The

relative positions of the lower and upper alignment markers are indicated.

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Section 4Troubleshooting

For more troubleshooting tips, refer to the Experion electrophoresisstation instruction manual and the Experion software help file.

4.1 Electrophoresis, Vortex, and Priming Stations

IV Check Failure message(s) displayed on computer screen:

One or more wells are not filled with the appropriate volume andthe electrode is not completely immersed. Make sure all samplewells are filled with 5 l of loading buffer and any unused samplewells contain 1 l loading buffer, TE, or DNase-free water

Air bubbles are interfering with the electrical contact in one or more

of the wells. Tap the chip or use a clean pipet tip to remove ordislodge the bubbles. When pipetting, insert the tip vertically,centered, and to the bottom of the well. Dispense the liquid slowly.Do not expel air at the end of the pipetting step. Visit the Bio-RadLaboratories website at www.bio-rad.com to view the Experion ChipLoading Training Video for proper loading technique. It can be found

at www.bio-rad.com/experionchiploading.

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Liquid has spilled from the chip during the vortex step. Inspect thearea outside the wells for signs of liquid. Ensure that the vortexstation platform is securely fastened to the base. If problem persists

contact Bio-Rad Laboratories

Check Seal message displayed on priming station:

Confirm that there is a chip in the priming station and that the chipis properly positioned on the platform

Check whether the O-ring gasket is clogged and/or replace theO-ring gasket in the priming station

4.2 DNA 1K Analysis

No peaks detected in lane on electropherogram:

An air bubble was introduced into the sample well or chip by poorpriming or sample loading technique. Inspect the back of the chipfor air bubbles in the channels after chip priming and in the wellsafter sample loading. Incomplete priming can also be caused bywrong priming conditions: Ensure setting C3, for DNA 1K analysis,was used

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Particulates are clogging channels. Use high-quality, 0.2 m filteredwater (such as Experion DEPC-treated water) or TE buffer andverify that the gel solution was properly filtered. Ensure chips are

kept free of dust and particulates; use powder-free gloves

Salt concentration in sample is too high. Refer to the specificationsin this manual (Section 1.3) for maximum concentration of salttolerated by the analysis. Dilute the sample if necessary

Electrode pin(s) are dirty, causing current leakage. Clean electrodepins using Experion electrode cleaner in a cleaning chip (seeAppendix for procedure) and/or perform the electrode manifolddeep cleaning protocol described in Bulletin 10001312

Laser or autofocus malfunction. Contact Bio-Rad Laboratories orperform the focus diagnostic test as described in the IQ/OQ

Validation Kit or the Security Edition Software

Small peaks in lane on electropherogram:

An air bubble is in the sample well. Check the chip for air bubblesafter sample loading

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Chip placed into instrument incorrectly. Ensure that the chip isseated properly in the electrophoresis station chip platform

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Late and/or missing upper marker peak in lane on electropherogram:

An air bubble is in the sample well. Check the chip for air bubbles

after sample loading Electrode pin(s) are dirty, causing current leakage. Clean electrode

pins using Experion electrode cleaner in a cleaning chip (seeAppendix for procedure) and/or perform the electrode manifolddeep cleaning protocol described in Bulletin 10001312

Sample not mixed completely by vortexer. Ensure vortex platform issecurely fastened to the base and power to the vortex meetsvoltage requirements. Premix sample with loading buffer to verifyinstrument problem and contact Bio-Rad Laboratories for repair ifnecessary

Upper marker digested by restriction enzyme. Add EDTA and/orheat sample to inactivate restriction enzyme prior to chip analysis

Channels are blocked by genomic or high molecular weight DNA.Review protocol for DNA isolation

DNA chips have expired. Ensure chips are used before expiration

date

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Broad and/or tailing peaks in lane on electropherogram:

An active restriction enzyme is in the sample. Add EDTA and/or

heat sample to inactivate restriction enzyme prior to chip analysis Electrode pin(s) are dirty, causing current leakage. Clean electrode

pins using Experion electrode cleaner in a cleaning chip (seeAppendix for procedure) and/or perform the electrode manifolddeep cleaning protocol described in Bulletin 10001312

Dye concentration is too high. Ensure DNA stain is completelythawed and thoroughly mixed before use. Ensure calibrated pipetsand the correct volume of stain was used duringpreparation of gel-stain (GS) solution

Dips in the baseline of a lane on electropherogram:

Sample concentration too high causing dye depletion. Load samplein proper range of concentrations (See Section 1.7)

Dye concentration is too low. Use calibrated pipets whendispensing stain, and follow the instructions for gel-stain preparation

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Setting used to prime chip was incorrect. Ensure setting C3 wasused for DNA 1K analysis

DNA chips have expired. Ensure chips are used before expirationdate

DNA fragment sizes are very different from expected sizes:

Ensure that there are 13 peaks in the ladder lane. Ensure thatcorrect peaks in ladder lane were selected and sample lane lower

and upper markers align with corresponding markers in the ladderlane. Manually set lower and/or upper marker as necessary

Poor overall chip performance:

There is an air bubble in the chip. Check the chip for air bubblesafter chip priming

Gel-Stain (GS) was pipetd into the wrong well during priming.Before priming, check to ensure correct loading of gel-stain solution

Priming station Replace Seal indicator light is on, but the chip wasstill used. Check or replace the O-ring

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Cold reagents were used. Ensure that kit reagents are warmed toroom temperature and mixed properly before use

Reagents have been degraded. Ensure that the reagents have notexpired and light-sensitive reagents have been protected from light

Clean the electrode with Experion electrode cleaner to remove anycontaminants

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Section 5Ordering Information

Catalog # Description700-7107 Experion DNA 1K Analysis Kit for 10 Chips, includes 10 DNA

chips, 3 x 250 l DNA 1K gel, 40 l DNA stain, 20 l DNA 1K

ladder, 750 l DNA 1K loading buffer, 3 spin filters

700-7163 Experion DNA Chips, 10, for DNA 1K and 12K analyses

700-7164 Experion DNA 1K Reagents and Supplies for 10 chips,includes 3 x 250 l DNA 1K gel, 40 l DNA stain, 20 l DNA 1K


700-7251 Experion Cleaning Chips, 10

700-7252 Experion Electrode Cleaner, 250 ml

700-7253 Experion DEPC-Treated Water, 100 ml

700-7254 Experion Spin Filters, 10

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Catalog # Description

Other Analysis Kits for the Experion Automated Electrophoresis

Station700-7108 Experion DNA 12K Analysis Kit for 10 Chips, includes 10 DNA

chips, 650 l DNA 12K gel, 40 l DNA stain, 20 l DNA 12K


700-7165 Experion DNA 12K Reagents and Supplies for 10 chips,

includes 650 l DNA 12K gel, 40 l DNA stain, 20 l DNA 12K


700-7103 Experion RNA StdSens Analysis Kit for 10 Chips, includes

10 RNA StdSens chips, 1,250 l RNA gel, 20 l RNA StdSens

stain, 20 l RNA ladder, 900 l RNA StdSens loading buffer,

2 spin filters

700-7104 Experion RNA StdSens Analysis Kit for 25 Chips, includes25 RNA StdSens chips, 2 x 1,250 l RNA gel, 2 x 20 l RNA

StdSens stain, 2 x 20 l RNA ladder, 2 x 900 l RNA StdSens

loading buffer, 4 spin filters

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700-7105 Experion RNA HighSens Analysis Kit for 10 Chips, includes

10 RNA HighSens chips, 1,250 l RNA gel, 20 l RNA HighSens

stain, 20 l RNA ladder, 900 l RNA HighSens loading buffer,

100 l RNA sensitivity enhancer, 2 spin filters

700-7106 Experion RNA HighSens Analysis Kit for 25 Chips, includes

25 RNA HighSens chips, 2 x 1,250 l RNA gel, 2 x 20 l RNA

HighSens stain, 1 x 20 l RNA ladder, 2 x 900 l RNA HighSens

loading buffer, 2 x 100 l RNA sensitivity enhancer, 4 spin filters

For a complete list of Experion products available, see our catalog or visit the website

at www.bio-rad.com.

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Section 6Legal Notices

LabChip and the LabChip logo are trademarks of Caliper Life Sciences,Inc. Bio-Rad Laboratories, Inc. is licensed by Caliper Life Sciences, Inc. tosell products using the LabChip technology for research use only. Dyeproducts are licensed under US Patent Nos. US 5,863,753, 5,658,751,5,436,134 and 5,582,947, and pending patent applications, and relatedforeign patents, for internal research and development use only in detecting,

quantitating, and sizing macromolecules, in combination with microfluidics,where internal research and development use expressly excludes the useof this product for providing medical, diagnostic, or any other testing, analysisor screening services, or providing clinical information or clinical analysis,in any event in return for compensation by an unrelated party.

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Section 7Appendix

7.1 How to Clean the Electrodes

This procedure should be performed when contamination of the electrodesis suspected. If the problem still persists, then perform the ElectrodeManifold Deep Cleaning procedure as described in the instrument manual.This protocol (Experion Bulletin 10001312) can also be downloaded from

the Bio-Rad Laboratories website.

1. Fill a cleaning chip with 800 l Experion electrode cleaner. Check tomake sure that there are no air bubbles trapped in the reservoir. Gentlytap the side of the cleaning chip to dispel any bubbles.

2. Open the lid of the electrophoresis station and place the chip on the

platform.

3. Close the lid and leave the chip in the instrument for 2 minutes.

4. Discard the electrode cleaning solution from the chip and thenthoroughly rinse the chip using DNase-free water. Dry the outside ofthe chip with a towel.

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Note: additional cleaning chips can be purchased (catalog #700-7251)if dedicated chips for the electrode cleaner and the DNase-free waterare desired.

5. Fill the cleaning chip with 850 l of DNase-free water and place it ontothe instrument chip platform.

6. Close the lid and leave the chip in the instrument for 5 minutes to rinsethe electrodes.

7. Replace the DNase-free water in the chip and repeat the rinse step.8. Open the lid and remove the chip containing water.

9. Leave the lid open for at least 2 minutes to allow any water remainingon the electrodes to evaporate.

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7.2 Quick Start Instructions

Turn on Experion electrophoresis station and launch Experion software

Equilibrate Kit Reagents to Room Temperature

Remove DNA 1K stain, gel (or gel-stain if available), and loading bufferfrom storage and equilibrate to room temperature

Invert each tube several times, vortex the contents and briefly centrifuge

Protect stain (gel-stain) from light at all timesPrepare the Gel-Stain Solution

Add exactly 12.5 l DNA stain (blue cap) to a tube of 250 l DNA 1Kgel (green cap). Vortex and briefly centrifuge.

Transfer gel-stain solution (GS) to a spin filter tube and centrifuge at

2,400 x g for 15 minutes.

Note: Filtered gel-stain stored at 4C may be used for up to 1 month

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Prepare the DNA Samples and 1K Ladder

Remove the DNA ladder (clear cap) from storage, briefly centrifugeand then vortex to mix. Place the tube of ladder on ice

Prepare dilutions of DNA sample in TE buffer or water as necessary forconcentration to be in linear range of the assay (0.150 ng/l total DNAconcentration) or if sample salt concentration is excessive (refer toSection 1.3 for maximum salt concentrations tolerated by the assay)

Priming the Chip

Remove a DNA chip from its packaging and place it on the chip platformin the Experion priming station

Add 9 l gel-stain solution into the highlighted well labeled GS (gelpriming well).

Close the lid of the priming station, set the pressure to C, and set thetime to 3

Press the Start button

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After priming is finished, remove the primed chip from the primingstation, flip it over, and visually inspect the microchannels for trappedair bubbles or incomplete priming

Load the Samples and DNA 1K Ladder Into the Chip

Pipet 9 l gel-stain solution into the other 3 wells labeled GS

Pipet 5 l loading buffer (yellow cap) into each sample well (111) andinto the ladder well, labeled L. Do not leave any sample well empty

Pipet 1 l DNA 1K ladder into the well labeled L

Pipet 1 l DNA sample into each of the 11 sample wells. Pipet 1 l TEbuffer or DNase-free water in any unused sample wells

Place the chip in the Experion vortex station. Vortex for 1 minute

Run the chip in the Experion electrophoresis station within 5 minutes ofloading

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Running the DNA 1K Analysis

Confirm the Experion electrophoresis station is on and the Experionsoftware is open

Place the loaded chip onto the electrophoresis station chip platform andclose the lid

Select New Run and the DNA 1K assay. Enter project name and runname prefix

Click on the Start arrow in the software. Select the number of samplesto run and select Start to begin the run

After the run is complete, remove and discard the used chip

Cleaning the Electrodes After a Run

Place a cleaning chip filled with 800 l DNase-free water into the

electrophoresis station

Close the lid for 60 seconds to clean the electrodes, and then open itfor 60 seconds to allow the electrodes to completely dry. Remove thecleaning chip and close the lid to the instrument

Change the water in the cleaning chip, and keep covered until next use

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10006453 Rev A

Life ScienceGroup

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Bio-Rad

Laboratories, Inc.

Web site www.bio-rad.com USA 800 4BIORAD Australia 02 9914 2800Austria 01 877 89 01 Belgium 09 385 55 11 Brazil55 21 3237 9400Canada 905 712 2771 China 86 21 6426 0808Czech Republic420 241 430 532 Denmark44 52 10 00

Finland09 804 22 00 France 01 47 95 69 65 Germany089 318 84 0Greece 30 210 777 4396 Hong Kong 852 2789 3300

Hungary36 1 455 8800 India 91 124 4029300/5013478 Israel03 963 6050Italy39 02 216091 Japan 03 5811 6270 Korea 82 2 3473 4460Mexico 55 5200 05 20 The Netherlands 0318 540666New Zealand64 9415 2280 Norway23 38 41 30 Poland48 22 331 99 99Portugal351 21 472 7700 Russia 7 095 721 14 04Singapore 65 6415 3188 South Africa 27 0861 246 723Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland061 717 95 55Taiwan 886 2 2578 7189/2578 7241 United Kingdom 020 8328 2000

Documents

Experion DNA 1K & 12K Analysis Kits