Protocols

Related Product Information

Introduction - E-Gel Electrophoresis System

The E-Gel® agarose gel electrophoresis system is a complete bufferless system for agarose gel electrophoresis of DNA samples.

The major components of the system are:

  • E-Gel® pre-cast agarose gels
  • Electrophoresis bases


E-Gel® pre-cast agarose gels are self-contained gels that include electrodes packaged inside a dry, disposable, UV-transparent cassette. The E-Gel® agarose gels run in a specially designed device that is a base and power supply combined into one device.
  
Advantages of E-Gel®

Using E-Gel® agarose gels for electrophoresis of DNA samples offer the following advantages:

  • Provides fast, safe, consistent, high-resolution electrophoresis
  • Eliminates the need to prepare agarose gels and buffers, and to stain gels
  • Compatible with most commercially available robotic systems for high-throughput agarose gel electrophoresis
  • Available in a variety of agarose percentages, well formats, and throughput to suit your applications

 

Medium/High-Throughput E-Gel® Electrophoresis System

The Medium/High-Throughput E-Gel® Electrophoresis System is designed for electrophoresis of 48-96 DNA samples per gel. This system is compatible for use with multichannel pipettors or automated liquid handling systems. For details on this system, see below.

The system consists of the following components:

E-Gel® 48 gels

Each E-Gel® 48 gel contains 48 sample lanes and 4 marker lanes and is designed for medium-throughput agarose electrophoresis of nucleic acids.

E-Gel® 96 gels

Each E-Gel® 96 gel contains 96 sample lanes and 8 marker lanes in a patented, staggered-well format and is designed for high-throughput agarose electrophoresis of nucleic acids.

E-Base™ Electrophoresis Device

The E-Base™ is a base and a power supply all in one device and is an easy-to-use, pre-programmed device specifically designed for electrophoresis of E-Gel® 48 and 96 gels.

E-Holder™ Platform

The E-Holder™ Platform is designed to hold E-Gel® 96 gels during robotic loading. The E-Holder™ is used to load multiple gels on a robotic platform while other gels are running on the E-Base™.

E-Editor™ 2.02 Software

The E-Editor™ 2.02 software allows you to quickly reconfigure digital images of E-Gel®  48 or 96 gel results for analysis and documentation. The E-Editor™ 2.02 software can be downloaded for free.
  
Choosing a Gel for Your Application

To obtain the best results for your application, it is important to choose the correct agarose percentage and well format.

The table below lists the various types of gel and resolution for each gel type.

Gel Type
No. Rows
No. Wells
Sample Volume
Run Length
Run Time
% Agarose
Resolution
E-Gel ®48 Gel
2*
48 sample
4 marker
10-15 µl
15 µl
3.2 cm
20 min.
1%
2%
4%
400 bp-10 kb
50 bp-3 kb
10 bp-400 bp
E-Gel ®96 Gel
8*
96 sample
8 marker
10-20 µl
20 µl
1.6 cm
12 min.
1%
2%
1 kb-10 kb
100 bp-2 kb


*Wells compatible for loading with a multichannel pipettor.

System Components

The Medium/High-Throughput E-Gel® Electrophoresis System is compatible for use with multichannel pipettors or automated liquid handling systems.

The system consists of the following components:

  • E-Gel® 48 gels and E-Gel® 96 gels
  • E-Holder™ Platform
  • E-Editor™ 2.02 Analysis Software


Applications

E-Gel® 48 and 96 agarose gels are suitable for analyzing multiple samples:

  • PCR products
  • Restriction digests
  • RT-PCR reactions
  • Primer immers (4% E-Gel® 48 gels)
  • Library screenings
  • Diced dsRNA (4% E-Gel® 48 gels)
  • SNPs analysis


E-Gel® 48 Gels

E-Gel® 48 gels are self-contained, pre-cast agarose gels that include agarose, a proprietary buffer system, ethidium bromide, and electrodes packaged inside a dry, disposable, UV-transparent cassette. Each E-Gel® 48 gel contains 48 sample lanes and 4 marker lanes and is designed for medium-throughput agarose electrophoresis of nucleic acids. This configuration provides a 3.2 cm run length.
 
The 4% E-Gel® 48 gels are prepared with high-resolution agarose to ensure quality resolution of DNA fragments below 400 bp. The wells of the E-Gel® 48 gel are compatible for loading with a multichannel pipettor. The lane numbers are labeled with fluorescent dye that transfers to the image and allows tracking of your samples during photo documentation of the gel.
 
In addition, each E-Gel® 48 cassette is labeled with an individual barcode to facilitate identification of the gel using commercial barcode readers.
 
Separation Range for E-Gel® 48 Gels

The separation range for E-Gel®48 gels is listed below:

Sample Range        
bp Separation
1% E-Gel®48
400 bp-600 bp              
50 bp
600 bp-1 kb           
100 bp
1 kb-4 kb             
500 bp
4 kb-10 kb               
1 kb
2% E-Gel®48
100 bp-300 bp         
25 bp
300 bp–700 bp          
50 bp
700 bp-1200 bp     
100 bp
1200 bp-2000 bp     
200 bp
4% E-Gel®48
5 bp-40 bp              
5 bp
40 bp-80 bp             
10 bp
80 bp-175 bp       
20 bp
175 bp-300 bp       
50 bp
300 bp-600 bp       
100 bp


E-Gel® 96 Gels

E-Gel® 96 gels are self-contained, pre-cast agarose gels that include agarose, a proprietary buffer system, ethidium bromide, and electrodes packaged inside a dry, disposable, UV-transparent cassette. Each E-Gel® 96 gel contains 96 sample lanes and 8 marker lanes in a patented, staggered-well format. The wells of the E-Gel® 96 gel are compatible with the standard 96-well plate format for automated loading.
 
In addition, each E-Gel® 96 cassette is labeled with an individual barcode to facilitate identification of the gel using commercial barcode readers. The lane numbers are labeled with fluorescent dye that transfers to the image and allows tracking of your samples during photo documentation of the gel.
 
During electrophoresis, samples migrate between the wells of the row below. For example, the bands of the lane B11 migrate between well C11 and C12. This configuration provides a 1.6 cm run length, allowing resolution between 100 bp and 10 kb. The staggered well format of the gel cassette is compatible with automated liquid handling devices that use 8-, 12-, or 96-tip loaders. During sample loading, the samples will fall onto the slopes of the wells and be drawn into the wells by capillary force.
 
Diagram of E-Gel® 96 Cassette

A diagram of the E-Gel® 96 cassette is shown below.

A diagram of the E-Gel 96 cassette


E-Base™

Two types of bases are available from Invitrogen:
 
The Mother E-Base™ (Catalog no. EB-M03) has an electrical plug that can be connected directly to an electrical outlet and is used for electrophoresis of one  E-Gel® 48, E-Gel® 96, or E-PAGE™ 96 gels available from Invitrogen.
 
The Daughter E-Base™ (Catalog no. EB-D03) connects to the Mother E-Base™, and together they can be used for the electrophoresis of two or more, E-Gel® 48, E-Gel® 96, or E-PAGE™ 96 gels available from Invitrogen.
 
Note:   The Daughter E-Base™ does not have an electrical plug and cannot be used without a Mother E-Base™.
 
Mother E-Base™

Each Mother E-Base™ has a pwr/prg (power/program) button (right side) and a time button (left side) on the lower right side of the base. The lower left side of each Mother E-Base™ contains a light LED and a digital display. The gel cassette is inserted into the two electrode connections. The Mother E-Base™ is connected to an electrical outlet with the electrical plug.
 
The E-Base™ is pre-programmed with 2 programs specific for each gel type as described below:

ProgramGel TypeRun Parameters
EGE-Gel® 96Time: 12 minutes



                                                                  Mother E-Base™

Mother E-Base


Daughter E-Base™

The Daughter E-Base™ is similar to the Mother E-Base™ except the Daughter E-Base™ does not have an electrical cord and cannot be connected to an electrical outlet.
 
The Daughter E-Base™ is connected to a Mother E-Base™ or to another Daughter E-Base™ (already connected to a Mother E-Base™). Once connected to a Mother E-Base™, each Daughter E-Base™ is designed to function independently of the Mother E-Base™ or other Daughter E-Bases™.
 
                                                        Mother E-Base™/Daughter E-Base™



Mother E-Base/Daughter E-Base

E-Holder™ Platform

The E-Holder™ Platform is designed to hold E-Gel® 96 gels during robotic loading. Use the E-Holder™ when you need to load multiple gels on a robotic platform while the other gels are running on the E-Base™.
 
Note:   The E-Holder™ is not a power supply unit, cannot be connected to an electrical outlet, and cannot be used to run gels.
 
E-Editor™ 2.02 Software

The E-Editor™ 2.02 software allows you to quickly reconfigure digital images of E-Gel® 48 or 96 gel results for analysis and documentation.
 
Capture an image of the gel and then, use the E-Editor™ 2.02 software to:

Align and arrange the lanes in the image
Save the reconfigured image for further analysis
Copy and paste selected lanes or the entire image into other applications for printing, saving, e-mailing, and/or publishing on the Web.

E-Editor™ 2.02 software can be downloaded for free from our Web site. Follow the instructions to download the software and user manual.
 

Product Specifications
 
E-Gel® 48 Gel Specifications
Each E-Gel® 48 gel contains 48 sample wells and 4 marker wells (M).

Cassette Size                             
13.5 cm (l) x 10.8 cm (w) x0.67 cm  (thick)
Gel Thickness                             
3.7 mm
Gel Volume              
50 ml
Gel Percentage                           
1%, 2%, and 4%
Well Depth                                
3 mm
Dimensions of the Well                      
3.6 mm (l) x 2.2 mm (w)
Running Distance
(one well to the next)    
32 mm
Space between Well Center          
 

 

Sample Preparation for E-Gel® 48/96 Gels

Introduction

For optimal results, follow the guidelines for preparing your DNA sample as described in this section.
 
Materials Needed

  • DNA sample
  • Loading buffer (optional)
  • Molecular weight markers 


Amount of DNA

Use 20-100 ng DNA per band for samples containing one unique band, or up to 500 ng per lane for samples containing multiple bands. If you are unsure how much to use, test a range of concentrations to determine the optimal concentration for your particular sample. Excess DNA will cause poor resolution.
 
Loading Method

The DNA samples are loaded in E-Gel® agarose gels using the One-Step Loading or Two-Step Loading method.
The One-Step Loading method is routinely used to load E-Gel® agarose gels.  The Two-Step Loading method is used to load E-Gel® agarose gels, if the One-Step Loading method produces fuzzy or indistinct bands, or the gel was removed from its plastic pouch for more than 30 minutes. Prepare loading buffer and sample volumes based on the loading method as described below.
 
Total Sample Volume

The recommended total sample volume for each gel type is listed in the table below.
Note:  For best results, keep all sample volumes uniform. If you do not have enough samples to load all wells of the gel, load an equal volume of buffer containing the same salt concentration as samples into any empty wells.

Gel Type
One-Step Loading
Two-Step Loading
E-Gel ®48 gel
15 µl
10 µl
E-Gel ®96 gel
20 µl
10 µl


Loading Buffer

Loading buffer is optional for One-Step Loading method but is required for the Two-Step Loading method for E-Gels

You can load your samples directly into the wells, if no loading buffer is used. If you are using loading buffer, mix the required amount of DNA with the loading buffer (see preparing samples).

We recommend using a loading buffer with the following formulation:

For One-Step Loading method, use a loading buffer that yields a final concentration of 10 mM Tris-HCl, pH 7.5; 1 mM EDTA; 0.005% bromophenol blue; 0.005% xylene cyanol FF.

For Two-Step Loading method, use a loading buffer that yields a final concentration of 10% glycerol (or 6% Ficoll 400) 10 mM Tris-HCl, pH 7.5; 1 mM EDTA; 0.005% bromophenol blue; 0.005% xylene cyanol FF

If you are using 10X BlueJuice™ Gel Loading Buffer or TrackIt™ Loading Buffer available from Invitrogen, dilute this buffer 50-to 200-fold to obtain optimal results with E-Gel® agarose gels. For Two-Step loading with 10X BlueJuice™ Gel Loading Buffer or TrackIt™ Loading Buffer dilute this buffer 50- to 200-fold and add 10% glycerol.
 
 
High Salt Samples

Important: To obtain the best results, prepare your high salt samples as described below.
 
Samples containing > 50 mM NaCl, 100 mM KCl, 10 mM acetate ions, or 10 mM EDTA (i.e. certain restriction enzyme and PCR buffers) will cause loss of resolution on E-Gel® agarose gels. Dilute samples 2- to 20-fold as described:

  • Restriction Digests Digest 500 ng-1 µg of DNA in 20 µl final volume. Use 1 µl (for samples >1 kb) or 5-10 µl (for samples <1 kb) and dilute as described below.
  • PCR Samples - Use 1-5 µl of a 50 µl reaction and dilute as described below.

 

Gel Type
One-Step Loading
Two-Step Loading
E-Gel ®48 gel
15 µl
10 µl
E-Gel ®96 gel
20 µl
10 µl


Preparing Samples

Prepare your samples based on the loading method used as described below:

 
One-Step Loading
Two-Step Loading
Total Sample Volume
E-Gel®48 gel: 15 µl
E-Gel®96 gel: 20 µl
Add deionized water to the required amount of DNA to bring the total sample volume to that listed above.
E-Gel®48 gel: 10 µl
E-Gel®96 gel: 10 µl
Mix the required amount of DNA with a glycerol loading buffer (see below) to obtain a final glycerol concentration of 10% in a total sample volume of 10 µl.
When loading into the gel, first load 5 µl (E-Gel ®48 gel) or 10 µl (E-Gel ®96 gel) of deionized water directly into each well and then add 10 µl of sample containing 10% glycerol.
Loading Buffer
Optional
Instead of water, you may use a loading buffer that yields a final concentration of 10 mM Tris-HCl; 1 mM EDTA, pH 7.5; 0.005% bromophenol blue; and 0.005% xylene cyanol FF.
To use 10X BlueJuice ™ TrackIt™ Loading Buffer, dilute this buffer 50- to 200-fold to obtain the optimal dye concentration. Gel Loading Buffer or or TrackIt ™ Loading Buffer, dilute this buffer 50- to 200-fold to obtain the optimal dye concentration.
Prepare a loading buffer that yields a final concentration of 10% glycerol (or 6% Ficoll 400), 10 mM Tris-HCl, pH 8.1; 1 mM EDTA, pH 7.5; 0.005% bromophenol blue; 0.005% xylene cyanol FF.
To use 10X BlueJuice™TrackIt™ Loading Buffer, dilute this buffer 50- to 200-fold and then add glycerol to a final concentration of 10% in the sample. Gel Loading Buffer or or TrackIt ™ Loading Buffer, dilute this buffer 50- to 200-fold to obtain the optimal dye concentration.


DNA Molecular Weight Markers

We recommend using the following DNA molecular weight markers for different types of E-Gel® agarose gels to obtain good resolution.
 
Note:   Supercoiled DNA molecular weight markers may produce a slightly fuzzy pattern when run on E-Gel® agarose gels containing ethidium bromide. Consider using Clear E-Gel® agarose gels and post-staining with ethidium bromide.

Product
Markers
Catalog no.
Amount Used
E-Gel®48 gels
1%
1 Kb Plus DNA Ladder
10787-018
Load 100-250 ng of markers in a volume of 15 µl in marker well. Use a buffer containing the same salt concentration as your samples.
    
 
TrackIt ™ 1 Kb Plus DNA Ladder
10488-085
 
 
500 bp DNA Ladder
10594-018
 
 
E-Gel ® High Range DNA Marker
12352-019
 
2%
TrackIt ™ 50 bp DNA Ladder
10488-043
 
 
TrackIt ™ 100 bp DNA Ladder
10488-058
 
 
50 bp DNA Ladder
10416-014
 
 
100 bp DNA Ladder
15628-019
 
 
Low DNA Mass Ladder
10068-013
 
 
E-Gel ® Low Range Quantitative DNA Marker
12373-031
 
4%
TrackIt ™ 25 bp DNA Ladder
10488-022
 
 
TrackIt ™ 50 bp DNA Ladder
10488-043
 
 
25 bp DNA Ladder
10597-011
 
 
50 bp DNA Ladder
10416-014
 
 
E-Gel ® Low Range Quantitative DNA Ladder
12373-031
 
E-Gel®96 gels
1%
E-Gel ®96 High Range DNA Marker
12352-019
Load 100-250 ng of markers in a volume of 20 µl in marker well. Use a buffer containing the same salt concentration as your samples.
2%
E-Gel ® Low Range Quantitative DNA Ladder
12373-031
 

 

Loading E-Gel® 48/96 Gels

Introduction

This section describes the procedure for loading and running samples on E-Gel® 48 and E-Gel® 96 gels using the Mother E-Base™ and Daughter E-Base™.

The Mother E-Base™ and Daughter E-Base™ are designed to fit most robotic platforms allowing you to load and run E-Gel® 48 and 96 Gels directly on the robot.

If you need to load multiple gels on a robotic platform while other gels are running on the E-Base™, use an E-Holder™ Platform.

The run time for the E-Gel® 96 gel is 12 minutes and E-Gel® 48 gels is 20 minutes.
 
The E-Gel® 48 and 96 gels can only be used once. Do not re-use.

The E-Gel® 48 and 96 gels are compatible with the E-Gel® 96 mother base and daughter base available previously from Invitrogen. For instructions on using the gels with E-Gel® 96 mother base and daughter base, see Running E-Gel® 48/96 Gels.
 

Using the Barcode

Each E-Gel® 48 and 96 gel is labeled with an individual barcode (with a number). The barcode facilitates identification of each gel cassette during the electrophoresis of multiple gels. Each E-Gel®48 and 96 gel contains an EAN 39 type of barcode, which is recognized by the majority of commercially available robotic barcode readers. Refer to the manufacturer’s instructions to set up the barcode reader.

Note:   When capturing an image of the E-Gel® 48 or 96 gel, note that the barcode label is easily overexposed. To ensure that the barcode label is distinct and readable in the image, experiment with different shutter settings for your particular camera.
 
 
Aligning the Robotic Loading Assembly

The wells of the E-Gel® 96 gel are staggered to provide maximum run length (see Figure 1, below). For proper loading of samples, it is important to program your robotic loading system to set the A1 tip of the 8, 12 or 96-tip robotic head over the E-Gel® 96 gel cassette as described below.

Set the position of the first tip, approximately 1 mm above the slope of the A1 well (see Figure 2, below). This will ensure that the remaining tips are aligned above the slopes of the remaining wells. Refer to the manufacturer’s manual of your robot to program this setting. After programming the setting, load your samples. During loading, the samples will fall onto the slopes of the wells and be drawn into the wells by capillary force.

E-Gel 96 gel cassette


For optimal results, load each E-Gel® 48 and 96 gel within 30 minutes of removing the gel from the plastic pouch and run the gel within 15 minutes of loading. If a gel has been out of its plastic pouch for more than 30 minutes, you must use the Two-Step Loading method described.
 
Do not pre-run E-Gel® 48 and 96 gels.

Store and run E-Gel® agarose gels at room temperature.
 
Selecting Program on E-Base™
The recommended program for E-Gel® is EG, and the run time for E-Gel® 48 gels is 20 minutes and E-Gel® 96 gels is 12 minutes.

You will need to select an appropriate program on the base prior to inserting a gel into the base. Note:   If you had previously set the E-Base™ to the desired program or set the time, the last used program or time is displayed.

  1. Plug the Mother E-Base™ into an electrical outlet using the plug on the base.  If using Daughter E-Base™, connect the Daughter E-Base™ to a Mother E-Base™ or to another Daughter E-Base™ connected to a Mother E-Base™.
  2. The display will show EP (default) or last program used (EG or EP).
  3. Select the appropriate program based on the gel: 

 

Gel TypeProgram
E-Gel® 96EG
 E-Gel® 48EG and then manually change time to 20 minutes by pressing and holding the time button until 2 minutes is displayed.


Setting the Time

The initial default time setting on an E-Base™ for program EG is 12 minutes. Follow instructions below to increase or decrease the time setting, if desired.
 
Do not run an E-Gel® 96 gel for more than 20 minutes or E-Gel® 48 gel for more than 30 minutes.

To increase or decrease the default run time when no cassette is inserted on the base, use the following steps:

  1. Connect the Mother E-Base™ to an electrical outlet. If you are using a Daughter E-Base™, connect the Daughter E-Base™ to the Mother E-Base™ and then connect the Mother E-Base™ to an electrical outlet.
  2. Press and release the time button located on the lower right corner of the base to view the time setting.
  3. Press and hold the time button to increase the time continuously.
  4. When you reach the desired default time, release the time button.


If the time button is not released, the time setting will increase until it reaches 00. To begin cycling through the numbers again, starting from 00, press the time button again.
 
Note:   To increase the run time when a cassette is inserted, press and release the time button to increase the time setting by 1-minute intervals or press and hold the time button to increase the time continuously.
 
To increase the run time while a run is in progress, see below. To manually interrupt or stop a run, see Running E-Gel® 48/96 Gels.
 
Inserting Gel in the E-Base™

Each E-Gel® 48 and 96 gel is supplied individually wrapped and ready for use. Use short, rigid tips for robotic loading.

To load your samples on the E-Holder™.

  1. Open the package and remove the gel.
  2. Remove the plastic comb from the gel.
  3. Slide the gel into the two electrode connections on the Mother E-Base™ or Daughter E-Base™. The two copper electrodes on the right side of the gel cassette must be in contact with the two electrode connections on the base, as shown below.
  4. When the gel is properly inserted into the base, a fan in the base will begin to run and a red light will illuminate at the lower left corner of the base. The digital display will show the appropriate time for a selected program or last time setting (Ready Mode). 


Holder



Note:   If you accidentally inserted a gel into the base before selecting program EG, remove the gel, select program EG, and then reinsert the gel in the base.
 
 
Method of Loading Samples

We recommend the following methods of sample loading based on the gel type:

GelType  
Method of Loading
E-Gel® 48Manual, multichannel pipettor (load samples into alternate wells of the gel followed by a second round of loading into the remaining wells), or robotic loading devices (8- or 12-tip)
E-Gel® 96 Manual, multichannel pipettor, or robotic loading devices (8-, 12-, or 96-tip)

Loading Gels

Load DNA samples into the gel using the One-Step Loading or Two-Step Loading method. Avoid introducing bubbles while loading, as they will cause the bands to distort. The One-Step Loading method is routinely used to load E-Gel ® 48 and 96 gels. If the One-Step Loading method produces fuzzy or indistinct bands, or the gel was removed from its plastic pouch for more than 30 minutes, use the Two-Step Loading method.
 
One-Step Loading Method

Load prepared samples into each well as described below:

  • For E-Gel® 48 Gels -- Load 15 µl of prepared sample into sample wells. Load 15 µl of sample buffer containing the same salt concentration as your sample into any remaining empty wells.
  • For E-Gel® 96 Gels -- Load 20 µl of sample into each well. Load 20 µl of sample buffer containing the same salt concentration as your sample into any remaining empty wells.


Two-Step Loading Method

First load deionized water into each well (including sample and empty wells). Then load prepared sample into each sample well. Do not premix. Load sample buffer containing the same salt concentration as your sample into any remaining empty wells.

  • For E-Gel® 48 Gels -- Load 5 µl of deionized water into all wells. Then load 10 µl of sample with 10% glycerol into sample wells and 10 µl of sample buffer containing the same salt concentration as your sample into any remaining empty wells.
  • For E-Gel® 96 Gels -- Load 15 µl deionized water into all wells. Then load 10 µl of sample with 10% glycerol into sample wells and 10 µl of sample buffer containing the same salt concentration as your sample into any remaining empty wells.

Load the appropriate DNA markers in the marker (M) wells of an E-Gel® 48 and 96 gels

Running E-Gel® 48/96 Gels

Using E-Base™

Instructions for running E-Gel® 48 and E-Gel® 96 gels in a Mother E-Base™ or Daughter E-Base™ are provided below.

Note:   It is not necessary to have a gel in the Mother E-Base™ if you are using a Daughter E-Base™. However, the Mother E-Base™ must be plugged into an electrical outlet.

  1. To begin electrophoresis, press and release the pwr/prg button located on the lower right corner of the Mother E-Base™.
    The red light will change to a green light and the digital display will show the count down time while the run is in progress. 

    Mother E-Base


    If you are using a Daughter E-Base™, press and release the pwr/prg button located on the lower right corner of the Daughter E-Base™

    Daughter E-Base


    To add to the run time while the run is in progress, press the time button to select the desired time and then release the time button.

    To interrupt or stop a run in progress, see below.

     
  2. The Mother E-Base™ or Daughter E-Base™ will signal the end of the run with a flashing red light and rapid beeping for 2 minutes followed by a single beep every minute.  At the end of the run, the digital display will show the original time setting (not any time change that was made during the electrophoresis). The digital display will also show the elapsed time (up to 19 minutes with a negative sign) since the end of the run.
  3. Press and release the pwr/prg button to stop the beeping. The light will turn to a steady red and the digital display will show the last time setting.
  4. Remove the gel cassette from the Mother E-Base™ or Daughter E-Base™. You are now ready to capture an image of the gel.



Note:    The bands in the gel will diffuse within 20-40 minutes.
 
 
We recommend that you disconnect the Mother E-Base™ from the electrical outlet when not in use for a prolonged period of time.
 
Interrupting an Electrophoresis Run

You can interrupt an electrophoresis run at any time by pressing and releasing the pwr/prg button to stop the current. The stopped current is indicated by a steady red light and the digital display will flash to indicate that the run was interrupted. You can remove the gel from the E-Base™ to check the progress of the run. Then:

  • To continue the run from the point at which it was stopped, reinsert the gel and press and release the pwr/prg button. The light changes to steady green and the digital display shows the count down time.
  • To cancel the rest of the interrupted run, press and hold the pwr/prg button for a few seconds. The digital display will reset and the base will return to Ready Mode. If desired, you can then program a new run time and rerun the gel.


In case of an external power failure (loss of electricity or the electrical cord is accidentally removed from the outlet), the run will continue when the power resumes. The Mother E-Base™ or Daughter E-Base™ will signal the end of the run as described above, except the light will be an alternating red/green to indicate that an external power failure had occurred during the run.
 
Maintaining E-Base™
The surfaces of the Mother E-Base™ and Daughter E-Base™ should be kept free of contaminants. To clean, disconnect bases from power source and wipe clean with a dry cloth. Do not attempt to open the Mother E-Base™ or Daughter E-Base™. To honor the warranty, bases should only be opened and serviced by Invitrogen.

Using E-Holder™ Platform

Introduction

The E-Holder™ Platform is designed to hold E-Gel® 48 and 96 gels during robotic loading. Use the E-Holder™ when you need to load multiple gels on a robotic platform while other gels are running on the E-Base™
Note: The E-Holder™ is not a power supply unit, cannot be connected to an electrical outlet, and cannot be used to run E-Gel® 96 gels.

To obtain the best results, run E-Gel® 48 or96 gels on the Mother E Base™ or Daughter E Base™ within 15 minutes after loading on E-Holder™.
  
Procedure

  1. Place the E-Holder™ on the robotic platform.
  2. Open the package and remove the E-Gel® 48 or 96 gel.
  3. Remove comb from the E-Gel® cassette.
  4. Place the E-Gel® cassette in the E-Holder™. Align the bottom left end of the cassette in the lower left alignment corner of the E-Holder™ as shown in the figure below.
  5. Set up your robotic system to load samples into the E-Gel® 48 or 96 gel placed on an E-Holder™. Program your robotic system to load the samples approximately 5 minutes before the previous electrophoresis run is complete. This will ensure that the loaded gel from the E-Holder™ will be placed onto an E-Base™ within the recommended time of 15 minutes.


E-Base

Results with E-Gel® 48 Gels

1% E-Gel® 48 Gel

Results obtained using a 1% E-Gel® 48 gel is shown in the figure below. The gel was electrophoresed for 23 minutes using the standard conditions described in this manual and imaged using a KODAK EDAS290 system.
You can use a mini transilluminator to view the bands. You may vary the amount of markers loaded on the gel to improve gel imaging.

E-Gel


The gel contains following samples:

LaneSample
1, 24, M (lower left, lower right)High Mass DNA Ladder (4 µl/well)
2, 3, 22, 23, 32, 33, 36, 37, 40, 41PCR product, 317 bp (100 ng/well)
4, 5, 20, 21, 30, 31,42, 43PCR product, 1 kb (100 ng/well)
6, 7, 18, 19, 28, 29, 44, 45PCR product, 3 kb (100 ng/well)
8, 9, 12, 13, 16, 17, 26, 27, 46, 47PCR product, 9 kb (100 ng/well)
10, 11, 14, 15, 34, 35, 38, 39E-Gel® High Range DNA Ladder (10 µl/well)
25, 48, M (upper right, upper left)1 Kb Plus DNA Ladder (0.5 µg/well)

 
2% E-Gel® 48 Gel

Results obtained using a 2% E-Gel® 48 gel is shown in the figure below. The gel was electrophoresed for 20 minutes using the standard conditions described in this manual and imaged using a KODAK EDAS290 system.
You can use a mini transilluminator to view the bands. You may vary the amount of markers loaded on the gel to improve gel imaging.

E-Gel


The gel contains following samples:

LaneSample
1, 24, M (lower left, lower right) 100 bp DNA Ladder (0.4 µg/well)
2, 3, 22, 23, 34, 35, 38, 39PCR product, 150 bp (100 ng/well)
4, 5, 8, 9, 20, 21, 40, 41PCR product, 240 bp (100 ng/well)
6, 7, 17, 18, 30, 31, 41, 42PCR product, 317 bp (100 ng/well)
8, 9, 16, 17, 28, 29, 44, 45PCR product, 1 kb (100 ng/well)
10, 11, 14, 15, 26, 27, 45, 47 PCR product, 3 kb (100 ng/well)
12, 13, 36, 37 E-Gel® 96 Low Range Quantitative Ladder (10 µl/well)
25, 48, M (upper left, upper right)50 bp DNA Ladder (0.4 µg/well)


 
 
4% E-Gel® 48 Gel

Results obtained using a 4% E-Gel® 48 gel is shown in the figure below. The gel was electrophoresed for 20 minutes using the standard conditions described in this manual and imaged using a KODAK EDAS290 system. You can use a mini transilluminator to view the bands. You may vary the amount of markers loaded on the gel to improve gel imaging.

E-Gel

The gel contains following samples:

LaneSample
46, 47, M (upper left) 10 bp DNA Ladder (1 µg/well)
1, 20, 21, 38, 39, 48, M (lower right)25 bp DNA Ladder (0.5 µg/well)
24, 25, M (lower left)50 bp DNA Ladder (0.5 µg/well)
26, 27, M (upper right)100 bp DNA Ladder (0.5 µg/well)
8, 13, 14, 34, 35  (10 µl/well)E-Gel® Low Range Quantitative DNA Ladder
2,3Synthetic 21-mer siRNA
(short interfering RNA, 100 ng/well)
6,7 dsRNA diced (cut) with Dicer enzyme (100 ng/well)
4,5Undiced dsRNA (100 ng/well)
22ssDNA, 60 mer (200 ng/well)
23ssDNA (lane 22) annealed to form dsDNA, 60 bp (100 ng/well)
9, 10, 44, 45PCR product Hinf I cut
11, 12, 36, 37PCR product Aat II cut
15, 28, 29PCR product, 40 bp (100 ng/well)
16, 30, 31PCR product, 72 bp (100 ng/well)
17, 32, 33PCR product, 150 bp (100 ng/well)
18, 40, 41PCR product, 240 bp (100 ng/well)
19, 42, 43PCR product, 317 bp (100 ng/well)

 

Results with E-Gel® 96 Gels

 

1% E-Gel® 96 Gel

Results obtained using a 1% E-Gel ® 96 gel are shown in the figure below. The gel was electrophoresed for 12 minutes using the standard conditions described in this manual and imaged using a KODAK EDAS120 system.
You can use a mini transilluminator to view the bands. You can vary the amount of markers loaded to improve gel imaging.

Note:    The wells of the E-Gel ® 96 gel are staggered. DNA bands migrate between adjacent wells in the row below. For example, the bands of lane A2 will migrate between wells B1 and B2.
E-Gel

The gel contains the following samples:
 
Lane                                                      Sample
1, 2, 3                                                    1 kb PCR product (100 ng)
4, 5, 6, 10, 11, 12                                  3 kb PCR product (100 ng)
7, 8, 9                                                    9 kb PCR product (100 ng)
M                                                           E-Gel ® High Range DNA Marker
 
 
2% E-Gel® 96 Gel

Results obtained using a 2% E-Gel ® 96 gel are shown in the figure below. The gel was electrophoresed for 12 minutes using the standard conditions described in this manual and imaged using a KODAK EDAS120 system.
You can use a mini transilluminator to view the bands. You can vary the amount of markers loaded to improve gel imaging.


E-Gel


The gel contains the following samples:
 
Lane                                                              Sample
1, 2, 3, 10, 11, 12                                         125 bp PCR product (100 ng)
4, 5, 6                                                            240 bp PCR product (100 ng)
7, 8, 9                                                            1 kb PCR product (100 ng)
M                                                                    E-Gel ® Low Range Quantitative DNA Ladder

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Using E-Editor™ 2.02 Software

Introduction

The E-Editor™ 2.02 software for Windows ® allows you to reconfigure digital images of E-Gel ® 48 and E-Gel ® 96 gels for analysis and documentation. The staggered lanes in an E-Gel ® 96 gels are difficult to compare and analyze by standard 1-D gel analysis programs such as Bio-Rad’s Quantity One, Phoretix 1D, or Kodak 1D software. E-Editor™ 2.02 software reconfigures the wells of an E-Gel ® 48 and E-Gel ® 96 gel into a side-by-side format for easy comparison and analysis.

You can reconfigure gels that were scanned in the original gel cassette, or gels that were removed from the cassette. You can also group the images of multiple gels loaded from a 384-well microtiter plate into a single image with a layout corresponding to that of the original plate.

Capture an image of the gel as described below and then, use the E-Editor™ 2.02 software to:

  • Align and arrange the lanes in the image
  • Save the reconfigured image for further analysis
  • Copy and paste selected lanes or the entire reconfigured image into other applications for printing, saving, e-mailing, and/or publishing on the Web
 
Imaging the Gel

Use an appropriate gel documentation system to capture a digital image of the gel. When imaging, the gel should be properly aligned (i.e., not at an angle) and gel features should be clear and distinct. Proceed to Downloading Software.
 
Downloading Software

E-Editor™ 2.02 software can be downloaded here and follow the instructions to download the software and user manual.
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Troubleshooting

The table below provides some solutions to possible problems you might encounter during the electrophoresis of E-Gel® 48 and 96 agarose gels.

Problem
Cause
Solution
No current
Daughter E-Base ™ used without Mother E-Base ™
Do not use the Daughter E-Base ™ without a Mother E-Base ™. The Daughter E-Base ™ does not have an electrical plug to connect to an electrical outlet.
 
Copper contacts in the base are damaged due to improper use
Make sure the copper contacts in the base are intact.
 
Expired or defective gel cassette used
Use fresh gel cassette. Use properly stored gels before the specified expiration date.
 
Gel cassette is not inserted properly into a base
Remove cassette and reinsert; a red light illuminates at the lower left corner of the base, a fan in the base begins to run, and digital display indicates time for a selected program or last time setting (Ready Mode) when the gel is properly inserted into the base.
Poor resolution or smearing of bands
Sample is overloaded
Do not load more than 20-100 ng of sample DNA per band. Less DNA is required since E-Gel ® agarose gels are thinner.
 
High salt concentration
Dilute your high-salt samples as described.
 
Very low volumes of sample loaded or sample was not loaded properly
Avoid introducing bubbles while loading the samples. Bubbles will cause band distortion.
Load the recommended sample volume based on the gel type and loading method.
For proper band separation, we recommend keeping sample volumes uniform. Load an equal volume of sample buffer containing the same salt concentration as your sample into the empty wells.
 
Gel was not electrophoresed immediately after sample loading
For best results, run the gel within 15 minutes of sample loading.
If you cannot run the gel immediately after sample loading, use the Two-Step Loading method.
If you are using the E-Holder ™, program your robotic system to load the gel 5 minutes before the end of the previous gel’s run.
 
A1 tip not aligned
Be sure to align the A1 tip properly prior to loading your samples on an E-Gel ®96 gel.
 
Expired gel used
Use properly stored gels before the specified expiration date.
 
Longer electrophoresis run time or high current during the run
Longer run times cause an increase in the current, resulting in poor band migration. Do not run the gel longer than the recommended time for each gel type.
Uneven run on E-Gel ®48 gels
Differential salt concentration in adjacent lanes
Be sure to load 15 µl of sample buffer containing the same salt concentration as the sample into any remaining empty wells.
Keep all sample volumes uniform.
Slanted bands in marker lanes on E-Gel ®48 gels
Differential salt concentrations in adjacent lanes
Prepare the marker in a buffer containing the same salt concentration as the samples.
Sample leaking from the wells
Sample is overloaded
Be sure to load the recommended volume of sample per well.
  
Use the Two-Step Loading method.
 
Wells damaged during comb removal
Be sure to remove the comb gently without damaging the wells.
Over-run the gel or need more time to run gel
Accidentally selected a different program
Select EG if you are using E-Gel ®96 gels. For E-Gel ®48 gels, select EG and then manually change the time to 20 minutes.
If you accidentally selected a different program and are at the beginning of the run, stop the run and select the desired program.
If you are well into the run, check the gel to see where the loading dye is running. Estimate the amount of time remaining and then manually stop the run.
Failure Mode indicated by a steady red and continuous rapid beeping, and flashing “ER” on an E-Base ™
Defective cassette
Disconnect the base and replace gel cassette with a fresh gel cassette.
Press and release the power button to return to Ready Mode.
 
Cold cassette
Use a room temperature cassette stored at room temperature. Avoid storing gel cassettes at 4°C.
 
Improper operating conditions
Use the E-Base ™ at room temperature (20-25°C).

E-Base™ Quick Reference Guide

Introduction
 
A quick reference guide for operating the Mother E-Base™ and Daughter E-Base™ is provided below. Operating modes and electrophoresis runs are described.

Mode
Action
Sound
Light
Digital Display
Base plugged in
Mother E-Base ™ connected to an electrical outlet
1 beep
No light if a cassette is not inserted, or red light if a cassette is inserted
Without gel cassette -EP, last program used (EP or EG) With gel cassette in -last time setting
Ready (with no current flowing through gel)
Gel cassette inserted into a base
--
Steady red
Default time setting (12 minutes for EG, 14 minutes for EP, or last time setting)
Run
Press and release the pwr/prg button
--
Steady green
Count down time
End of run
Automatic
Continuous beeping for 2 minutes followed by a single beep every minute
Flashing red until the time button is pressed
Negative time display (00 to
-19 minutes)
Run ends after an external power failure
Automatic
Continuous beeping for 2 minutes followed by a single beep every minute
Alternating red and green
Negative time display (00 to
-19 minutes)
Pause (manually end the run)
Press and release the pwr/prg button during the run
--
With gel cassette in - steady red
Without gel cassette - no light
Flashing time display
Return to Ready mode after an automatic stop
Press and release the pwr/prg button
--
Steady red
Last time setting
Restart after a manual stop
Press and release the pwr/prg button
--
Steady green
Count down time
Return to Ready mode after a manual stop
Press and hold the pwr/prg button
--
With gel cassette in – steady red
Without gel cassette – no light
With gel cassette in –last time setting
Without gel cassette - last program setting
Failure
Press and hold pwr/prg button for 2 seconds and remove gel from the base
Continuous loud beeping
 
Flashing “ER”
No cassette
--
--
--
EP, last program used (EP or EG)
Time setting
With gel cassette in - Press and release the time button
--
With gel cassette – steady red
Time increases by 1 minute increments
With and without gel cassette - Press and hold the time button
--
With gel cassette in – steady red
Without gel cassette – no light
Time increases continuously and automatically stops at 00
Program setting
Press and release the pwr/prg button when no cassette is inserted into the E-Base™ to select the desired program
1 beep
No light
Selected program EP or EG

Explanation of Symbols and Warnings

symbol

The Mother E-Base™ and Daughter E-Base™ comply with the Underwriters Laboratories Inc. regulation and the European Community Safety requirements. Operation of the E-Gel® bases is subject to the following conditions:

  • Indoor use.
  • Altitude below 2,000 meters.
  • Temperature range: 5° to 40°C.
  • Maximum relative humidity: 80%.
  • Installation categories (over voltage categories)   II; Pollution degree 2
  • Mains supply voltage fluctuations not to exceed 10% of the nominal voltage (100–240V, 50/60Hz, 1500 mA).
  • The Mother E-Base™ has been tested with up to 3 Daughter E-Bases™ connected at one time.
  • Mains plug is a disconnect device and must be easily accessible.
  • Do not attempt to open E-Base™ devices. To honor the warranty, E-Base™ can only be opened and serviced by Invitrogen.
  • The protection provided by the equipment may be impaired if the equipment is used in a manner not specified by Invitrogen.


Ethrog Biotechnologies Ltd., an Invitrogen company, is the manufacturer and owner of the UL file. For more information, contact:

Ethrog Biotechnologies Ltd.
Ness-Ziona Science Park
Bldg 14, P.O. Box 444
Ness-Ziona, Israel 74103

symbol

The Caution symbol denotes a risk of safety hazard. Refer to accompanying documentation.


symbol

Double Insulation
Class II product


symbol


E-Gel® PowerBase



The E-Gel® PowerBase™ complies with the Underwriters Laboratories Inc. regulation and is listed under file no. E189045 in the U.S. and Canada.
This device complies with part 15 of the FCC Rules. Operation is subject to the following two conditions:

  • This device may not cause harmful interference.
  • This device must accept any interference received, including interference that may cause undesired operation.

 

LT073