ThermoFisher Scientific invitrogen E-Base EBM03 User manual

QUICK REFERENCE Pub. No. MAN0018775 Rev. A.0
E-Base™Electrophoresis Device
Connecting a Daughter E-Base™Device
·For higher throughput, up to three E-Base™Daughter units can be connected to an
E-Base™Mother Device.
·IMPORTANT! Ensure the Mother E-Base™Device is unplugged before connecting
any Daughter E-Base™Devices.
Mother E-Base™Device with
Daughter E-Base™Device
Mother E-Base™Device with
multiple Daughter E-Base™Devices
Troubleshooting
For detailed troubleshooting instructions see the E-Base™Electrophoresis System User
Guide at thermosher.com or contact Technical Support.
Limited product warranty and licensing information
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Contents Catalog Numbers EBM03, EBD03
Product Cat. No. Amount
Mother E-Base™Device EBM03 1 each
Daughter E-Base™Device EBD03 1 each
Product description
·The E-Base™Device is an easy-to-use, programmable, automated small-footprint
device combining a base and power supply to simplify electrophoresis of precast
E-Gel™48, E-Gel™96, E-PAGE™48 and E-PAGE™96 gels.
·High-throughput and automation-compatible.
·Provides fast, safe, consistent, high-resolution electrophoresis.
·Eliminates the need to prepare agarose gels, buffers, and to stain gels.
Required materials
DNA analysis
·E-Gel™48 or 96 agarose gels (See Gel selection guide)
·E-Gel™DNA Ladder (See Ladder selection guide)
·UltraPure™DNase/RNase-Free Distilled Water (Cat. Nos. 10977015, 10977035)
·E-Gel™Imager System with Blue Light Base (Cat. No. 4466612)
·(Optional) 1X E-Gel™Sample Loading Buffer (Cat. No. 10482055)
·(Optional) Safe Imager™2.0 Blue-Light Transilluminator (Cat. No. G6600)
Protein Aanalysis
·E-PAGE™48 or 96 gels (See Gel selection guide)
·E-PAGE™SeeBlue™Pre-stained Standard (Cat. No. LC5700)
·E-PAGE™Loading Buffer 1 (Cat. No. EPBUF01)
Online
resources
∤Visit our product pages for protocols, safety, and additional
product information.
∤Go online to view related E-Gel™products.
∤For support, visit thermosher.com/support.
For Research Use Only. Not for use in diagnostic procedures.
Print Options

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1 July 2019 -2-
E-Base™DNA electrophoresis protocol
Important guidelines
·Use 10−200 ng DNA per band for samples with one unique band or up to 500 ng per lane for samples with multiple bands.
·Dilute samples with high salt concentrations (>50 mM NaCl, >100 mM KCl, >10 mM acetate ions, >10 mM EDTA) 2- to 5-fold in deionized water, TE, or 1X E-Gel™Sample Loading
Buffer, in a nal volume of 15 μL (48-well gels) or 20 uL (96-well gels).
·Load E-Gel™agarose gels within 30 minutes after opening the pouch; run gels within 1−3 minutes after loading samples.
Step Action
1–5 min
1Prepare samples
Prepare DNA samples in deionized water OR 1X E-Gel™Sample Loading Buffer.
·For optimal separation use 20−100 ng of DNA per band for samples with one unique band or
up to 500 ng per lane for samples with multiple bands.
·The total sample volume for 48-well gels is 15 µL.
·The total sample volume for 96-well gels is 20 µL.
5–10 min
2
Prepare gel
cassette
a. Plug the Mother E-Base™Device into an electrical outlet.
b. Remove the gel from the package and gently remove the comb(s) from the E-Gel™cassette.
c. Insert the cassette into the E-Base™Device, starting from the right edge. When properly
inserted, the device indicates its initialized status with a steady red light.
Note:The protocol type on the display shows EG for E-Gel™DNA cassettes, and EP for
E PAGE™cassettes.
3Load samples
Load samples with a multichannel pipettor.
Load a volume of 15 μL in each well for 48-well gels.
Load a volume of 20 μL in each well for 96-well gels.
a. Load prepared samples into sample wells. Keep all sample volumes uniform.
b. Load prepared E-Gel™DNA ladder into marker wells.
c. Load 1X E-Gel™Sample Loading Buffer or deionized water in all empty wells. The buffer for
empty wells should have a similar salt concentration to adjecent sample wells.

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1 July 2019 -3-
E-Base™DNA electrophoresis protocol
Step Action
12–30 min
4
Run the gel
a. Select the EG program (default run time 12 minutes) for running E-Gel™cassettes by
pressing and releasing the “pwr/prg”.
b. Select the recommended run time for a specific gel type by pressing and releasing the time
button, then press and hold the time button to increase the time. Release time button when
the desired run time for the gel is reached.
Gel type Recommended run time Maximum run time
E-Gel™48 agarose gel 20 min 25 min
E-Gel™96 agarose gel 12 min 17 min
c. Start the run by pressing and releasing the “pwr/prg” button. The red indicator light will
change to green.
5End the run
a. A flashing red indicator light and rapid beeping indicates the end of the run. Press and
release “pwr/prg” to stop the device.
b. For better detection sensitivity, allow the gel to cool down for 10 minutes after the end of
the run.
1–2 min
6
Analyze the gel
a. Visualize the with a DNA imager using blue-light transillumination (e.g., with the E-Gel™
Imager System with Blue Light Base).
·SYBR Safe™DNA gel stain has an excitation maxima at 280 and 502 nm, and an emission
maximum at 530 nm when bound to nucleic acid.
·Use the E-Editor™2.0 software available at thermofisher.com/egel to analyze 96-well
format digital images.

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1 July 2019 -4-
E-Base™protein electrophoresis protocol
Important guidelines
·E-PAGE™Gels contain SDS and are designed for electrophoresis under denaturing conditions.
·Dilute samples with high salt or detergent concentrations to prevent loss of resolution. See Table of recommended nal concentrations.
·For optimal separation use up to 20 μg of protein per well. Limit the protein (or lipid) amount in the sample to 2 µg/µL in the nal sample volume for a proper LDS to protein ratio.
Step Action
1–5 min
1Prepare samples
a. Prepare protein samples in a total volume of 10 µL according to the following table. Scale
volumes according the to the required sample volume.
·The total sample volume for 48-well gels is 10 µL.
·The total sample volume for 96-well gels is 15 µL.
Reagent Reduced Non-reduced
Protein sample xµL xµL
4X E-PAGE™Loading Buffer 1 2.5 µL 2.5 µL
10X NuPAGE™Sample Reducing Agent 1 µL 
Deionized water to 10 µL to 10 µL
b. Incubate the samples at 70°C for 10 minutes.
5–10 min
2
Prepare gel
cassette
a. Remove the gel from the package and gently remove the combs from the E-PAGE™cassette.
b. Insert the cassette into the E-Base™Device, starting from the right edge. When properly
inserted, the device indicates its initialized status with a steady red light.
Note:The protocol type on the display shows EG for E-Gel™DNA cassettes, and EP for
E-PAGE™cassettes.
3Load samples
Load samples with a multichannel pipettor.
Load a volume of 10 μL in each well for 48-well gels.
Load a volume of 15 μL in each well for 96-well gels.
a. Load 510 µL of deionized water into all wells prior to adding samples or standards.
b. Load prepared samples into sample wells. Keep all sample volumes uniform.
c. Load prepared E-PAGE™standard into marker wells.
d. Load deionized water in all empty wells.

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1 July 2019 -5-
E-Base™protein electrophoresis protocol
Step Action
14–30 min
4
Run the gel
a. Select the EP program (default run time 14 minutes) for running E-PAGE™cassettes by
pressing and releasing the “pwr/prg”.
b. Select the recommended run time for a specific gel type by pressing and releasing the time
button, then press and hold the time button to increase the time. Release time button when
the desired run time for the gel is reached.
Gel type Recommended run time Maximum run time
E-PAGE™48 gel 25 min 30 min
E-PAGE™96 gel 14 min 25 min
c. Start the run by pressing and releasing the “pwr/prg” button. The red indicator light will
change to green.
5End the run
a. A flashing red indicator light and rapid beeping indicates the end of the run. Press and
release “pwr/prg” to stop the device.
b. For better detection sensitivity, allow the gel to cool down for 10 minutes after the end of
the run.
1–2 hr
6
Stain the gel
a. Open the gel cassette.
b. Visualize the protein by staining the gel using any of the following techniques (See the
E-PAGE™Technical Guide for details on staining and imaging).
·SYPRO™Ruby Protein Gel Stain protocol
·Coomassie R-250 protocol
·SimplyBlue™SafeStain protocol
·SilverQuest™Silver Stain protocol
·SilverXpress™Silver Stain protocol

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1 July 2019 -6-
Gel selection guide
Application Product Gel % Sample wells In-gel stain [1] Amount Cat. No.
DNA sample analysis E-Gel™48 Agarose Gels, 1% 1% 48 + 4 ladder lanes SYBR Safe™8 gels G820801
4 x 8 gels G820841
E-Gel™48 Agarose Gels, 2% 2% 48 + 4 ladder lanes SYBR Safe™8 gels G820802
4 x 8 gels G820842
E-Gel™96 Agarose Gels, 1% 1% 96 + 8 ladder lanes SYBR Safe™8 gels G720801
4 x 8 gels G720841
E-Gel™96 Agarose Gels, 2% 2% 96 + 8 ladder lanes SYBR Safe™8 gels G720802
4 x 8 gels G720842
Protein sample analysis E-PAGE™8% Protein Gels, 48-well 8% 48 + 4 ladder lanes — 8 gels EP4808
E-PAGE™6% Protein Gels, 96-well 6% 96 + 8 ladder lanes — 8 gels EP9606
[1] For other stain options visit thermofisher.com/egel.
Ladder selection guide
Product Recommended DNA ladder
E-Gel™96 High Range DNA Lad-
der
(Cat. No. 12352019)
E-Gel™50 bp
DNA Ladder
(Cat. No. 10488099)
E-Gel™Low Range Quantitative
DNA Ladder
(Cat. No. 12373031)
E-Gel™48 Agarose Gels, 1% 4— —
E-Gel™48 Agarose Gels, 2% — 4—
E-Gel™96 Agarose Gels, 1% 4— —
E-Gel™96 Agarose Gels, 2% — — 4
For more ladder options visit thermofisher.com/egelladders.