SGI-DNA BIOXP 3200 User manual

BioXp™3200 System
User's Guide
REV. 5.0 01.08.19
Part number 40010

LEGAL NOTICES
Limited Use Label License Except as otherwise agreed in writing by our authorized representative, this product is for INTERNAL RESEARCH USE
ONLY AND NOT FOR HUMAN, ANIMAL, THERAPEUTIC OR DIAGNOSTIC USE. For additional information about your
rights under this research license, please see our website at sgidna.com.
Limited Warranty a) SGI-DNA's entire liability and your exclusive remedy if the Product fails to conform to the following warranty (a
“Nonconforming Product”) shall be, at SGI-DNA's sole option, either repair or replacement of such Nonconforming
Product, or, if neither is practicable, a refund of the fees paid for the Product. The warranty for the repaired or
replaced Product is limited to the scope and remaining duration of the original warranty for the Nonconforming
product or, if longer, for 30 days after the date of shipment to you of the repaired or replaced Product. The warranty
is contingent upon proper use of the Product in accordance with the User's Guide and does not apply to any Product
that is subjected to unusual physical or electrical stress, misuse, neglect, improper testing or storage, modication or
unauthorized repair or upgrade.
b) SGI-DNA warrants that the product, as delivered, will be free from defects in material and workmanship for a
period of one year from the date it is delivered to you (“the Warranty Period”).
c) This warranty gives you specic legal rights and you may have other legal rights which vary from state to state.
This warranty is non-transferable.
d) OTHER THAN AS EXPRESSLY SET FORTH ABOVE, SGI-DNA MAKES NO WARRANTIES, EXPRESS, STATUTORY,
IMPLIED, OR OTHERWISE. NO DISTRIBUTOR, AGENT OR EMPLOYEE IS AUTHORIZED TO MAKE ANY MODIFICATIONS,
EXTENSIONS OR ADDITIONS TO THIS WARRANTY.
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out of i) any warranty of greater scope or duration than that set forth in this SGI-DNA Limited Warranty; and ii) failure
to disclaim implied warranties and limit remedies and liabilities, by and on behalf of SGI-DNA.
Trademark Information TipOne® is a registered trademark of USA Scientic, Inc.
Gibson Assembly® is a registered trademark and BioXp™, Oligo Vault™, and Bio360™ are trademarks of SGI-DNA.
E. cloni® is a registered trademark of Lucigen Corporation.
TransforMax™ and EPI300™ are trademarks of Epicentre, Madison, Wisconsin.
Gene Pulser® is a registered trademark and Xcell™ is a trademark of Bio-Rad Laboratories, Inc.
Qubit® is a registered trademark and Nunc™ is a trademark of Thermo Fisher Scientic Inc.
Q5® and OneTaq® are registered trademarks of New England BioLabs, Inc.
Regulatory Statement For Research Use Only
Statement of Proprietary
Information
Copyright in this work is vested in SGI-DNA and the document is issued in condence for the purpose only for
which it is supplied. It must not be reproduced in whole or in part except under an agreement or with the consent
in writing of SGI-DNA and then only on the condition that this notice is included in any such reproduction. No
information as to the contents or subject matter of this document or any part thereof arising directly or indirectly
there from shall be given orally or in writing or communicated in any manner whatsoever to any third party being an
individual rm or company or any employee thereof without the prior consent in writing of SGI-DNA.
Terms and Conditions IMPORTANT- This agreement (the “Agreement”) is a legal agreement between you and SGI-DNA. By installing or
otherwise using the BioXp™ 3200 System (referred in this agreement as the “Product”), you agree to be bound by the
terms of this Agreement. If you do not wish to be bound by the terms of this Agreement, do not use the Product and
promptly return the unused, unopened Product to the place of purchase for a full refund. The user is prohibited from
reverse engineering the software or output les generated from the BioXp™ 3200 system.
Limitation of Liability SGI-DNA'S LIABILITY ARISING OUT OF OR RELATING TO A PRODUCT SHALL NOT EXCEED THE AGGREGATE AMOUNTS
YOU PAID TO SGI-DNA FOR THE PRODUCT. IN NO EVENT WILL SGI-DNA BE LIABLE FOR LOST USE, PROFITS, REVENUE,
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Disclaimer The material in this manual is for informational purposes only and is subject to change without prior notice at any
time. SGI-DNA and/or its aliates assume no responsibility for any errors that may appear in this document.
INDICATIONS FOR USE The BioXp™ 3200 System is a device which is intended for the processing of DNA materials. The system is not
approved for use other than that stated above.
Technical Services For technical assistance, please contact technical services at techser[email protected]om or 1-855-474-4362.
SGI-DNA
sgidna.com
©2019 SGI-DNA. All rights reserved.
Gibson Assembly®: US Patent Nos. 7,776,532, 8,435,736, and 8,968,999.
010819

Table of Contents
BioXp™ 3200 Instrument Guide 3
Instrument Ordering Information 3
Safety Information 3
Manual Symbols 3
Precautions 3
Marking Symbols on the Equipment 3
Safety Warnings 4
Equipment Specications 6
System Components 6
Technical Specications 6
Installation Guide 6
System Location 6
Unpacking, Set up, and Power Up 8
Getting to Know the System 9
Starting the BioXp™ System 10
Ethernet Set Up 10
Start the BioXp™ System 10
Quick Start Guide: Performing an Instrument Run 11
BioXp™ Tiles and Libraries Quick Start 11
BioXp™ Cloning Quick Start 12
Operational Features of the BioXp™ System 15
Delay Start 15
Tracking Progress During a Run 16
Canceling a Job During Delay Start 17
Canceling a Job During a Run 17
Shutting down the BioXp™ System 17
Conguring the BioXp™ System 18
Instrument Troubleshooting 19
General Instrument Troubleshooting 19
Deck Inspection 19
Error Messages 19
Cleaning and Maintenance 20
Cleaning Instructions 20
Calibration 20
Preventative Maintenance 20
Repair 20
Recommended Separation Distances 20
Equipment Disposal 21
WEEE Compliance 21
Regulatory Statements 22
FCC Compliance Statement 22
Guidance and Manufacturer’s Declaration: Emissions 22
Guidance and Manufacturer’s Declaration: Immunity 22
1

BioXp™ Tiles, Libraries, and Clones 23
Product Ordering Information 23
Overview 23
Receiving an Order 23
Required materials (not included in the product order) 24
Specications 24
Consumables and Reagents 25
Instrument Operation 26
Preparing for a BioXp™ 3200 System run 26
Load the instrument 27
Begin the Run 28
During the Run 28
After the Run 28
Analyzing BioXp™ Tiles, Libraries, and Clones 30
Gel Electrophoresis 30
Next Steps– BioXp™ Tiles and Libraries 31
Quantication 31
Cloning BioXp™ Tiles 31
Multi-fragment Assembly 31
PCR Amplication (Optional) 32
Colony Screening (Optional) 33
Next Steps– BioXp™ Clones 34
Transformation 34
Full-length Clone (EFC) Analysis 36
Screening colonies 36
Reference Material 38
pUCGA 1.0 Amp clone map 38
Troubleshooting 39
2

3
BioXp™ 3200 Instrument Guide
Instrument Ordering Information
Product Description Cat. No.
BioXp™ 3200 System, includes 1 year warranty Standard Ethernet conguration of
BioXp™ Instrument
BX 3200-02 and
BX 3200-02 EU
BioXp™ 3200 System Service Contract, 1 year Covers parts and labor for instrument
failure for 1 year, renewable annually
BX 3200-05 and
BX 3200-05 EU
Safety Information
Manual Symbols
This manual describes the use and maintenance of the SGI-DNA BioXp™ 3200 Instrument. Read this
manual completely before putting the instrument into service. The following icons are used in this
manual:
Electrical Safety Warning: Failure to follow these instructions can cause
harm to operators or subjects.
Important Note: Failure to follow these instructions can lead to damage of
the system or unexpected results.
Precautions
• The BioXp™ System conforms to the following standards: IEC 61010-1:2001 2nd Edition to include
EN61010-1:2001, IEC/EN 61010-2-010, IEC/EN 61010-2-081.
• The radiation exposure hazard is non-critical.
Covers and exterior components which the operator may come in contact
with during routine maintenance or calibration, shall operate at a voltage
no greater than 25 V AC or 60 V DC.
Marking Symbols on the Equipment
Warning: Indicates a warning concerning operations that may lead to
personal injury or potential damage to the instrument if not performed
correctly.
Caution, Hot Surface, Do NOT Touch.
Conformité European: This mark is a declaration by the manufacturer
that the respective component complies with the relevant directives and
standards as issued by the European Union.
Alternating Current.
Waste Electrical and Electronic Equipment (WEEE) Directive: Do not
dispose symbol. See "Equipment Disposal" on page 21 for additional
information.
Consult instructions for use.

4
Safety Warnings
Installation
The BioXp™ System is heavy. Do not attempt to lift or move the instrument without
the assistance and supervision of colleagues. Be certain to use appropriate moving
equipment and proper lifting techniques (including but not limited to making certain
that you have a secure grip on the instrument before lifting, keeping your spine in
a neutral position while lifting with your legs, and coordinating lifting and moving
movements with all appropriate personnel). Improper lifting can cause permanent back
injury.
Use this product only as specied. If the instrument is used in a manner not specied
by SGI-DNA, the protection provided by the instrument may be impaired, resulting in
personal injury or damage to the instrument.
Ground Circuit Protection
Check the mains electricity supply plug, voltage, and frequency to conrm that the
supply corresponds to the values shown on the instrument label.
Ensure that the supply of power to the instrument is via a socket tted with a protection
device, such as a circuit breaker of the correct rating, to provide automatic power cut-o
in the cause of an insulation fault.
Conrm that the mains wiring is grounded. SGI-DNA declines all responsibility for any
damages due to instrument non-grounding.
Main Power Switch
Do not position the instrument such that it is dicult to operate the main power switch.
Hazardous Chemical Warning
Chemicals used with the instrument may be hazardous.
Always wear protective gear including safety goggles, gloves, and a lab coat when
handling chemicals.
Exercise caution when handling ammable liquids.
Take precautions, including but not limited to installing proper ventilation systems, to
ensure that the BioXp™ System laboratory is safe and that operators of the instrument
will not be exposed to hazardous levels of harmful chemicals.
Follow all national, state, and local health and safety regulations and laws.
Use proper waste disposal in accordance with all relevant regulations.
Refer to applicable Material Safety Data Sheets (MSDSs).
Flammable Liquids: Instrument Warning
Exercise caution when using ammable liquids in the BioXp™ System to minimize the risk
of re.
Do not use any ammable liquids in the instrument except for the liquids required in the
included procedure.
Provide adequate ventilation for the instrument to prevent the accumulation of
ammable vapors.
All sources of ignition, such as open ame or electrical spark, are not permitted near the
instrument or in areas where ammable vapors may travel.
Ensure that the instrument, all neighboring equipment, and users of the instrument are
appropriately grounded to minimize the generation of static electricity.
Do not use the Ethanol Reservoir if it is cracked.

5
Flammable Liquids: Solution Handling Warning
Keep ammable liquids in covered containers when not in use.
Provide means to promptly and safely dispose of any ammable liquid leaks or spills.
Do not transfer liquids using air pressure.
Read applicable MSDSs.
Store ammable liquids in cool, well-ventilated areas away from corrosives, oxidizers, and
ignition sources.
Label containers and cabinets as "ammable materials" where applicable.
Use only approved safety vessels for ammable liquid storage.
Ground and bond ammable liquid containers to prevent static charge build-up.
Never pour ammable liquids down a drain or sink.
Dispose of empty ammable containers in an approved manner.
Electrical Safety Warnings
Do not attach the power cord to an extension cord or to a multiple portable socket.
Doing so may compromise shielding and/or grounding.
This equipment should not be used adjacent to or stacked with other equipment. If it
becomes necessary to use the BioXp™ System under these conditions, the unit should be
observed to verify normal operation in this condition.
Use only grounded mains outlets for instrument supply.
Use only grounded mains outlets to supply instrument.
Do not remove any panels. Panels should be removed only by trained service personnel.
The AC power cord is the primary disconnection device for the instrument. Ensure that
the point of connection is easily accessible and free of any obstructions.
Important Warning: Moving Parts
Do not override the door lock. When the door is locked, the moving parts of the
instrument are operational. Never attempt to physically restrict movement of instrument
components.
Interfering with moving parts may cause personal injury. Keep hands clear of moving
parts while operating the instrument.
Do not move or shift the instrument during operation.
If the instrument shows evidence of corrosion or wear, do not attempt to manipulate or
tamper with components of the instrument.
Important Warning: Disconnecting the Instrument
Disconnect power to the system before cleaning or performing maintenance.
DO NOT remove any panels; panels should be removed only by qualied service
personnel.
Do not disassemble unit.

6
Equipment Specications
System Components
Use of other parts or materials other than those supplied with the instrument can degrade
system performance and may cause safety hazards. Use only SGI-DNA approved or supplied
components.
Use only SGI-DNA supplied Power Supply Cord. Use of other power cords may compromise
electrical protection and could create a hazard.
Components of the BioXp™ System
BioXp™ 3200 Instrument
Power Cord
RJ45 Ethernet Cable
Reagent and Recovery Plate Thermal Covers
Ethanol Reservoir
Technical Specications
Product Name BioXp™ 3200 System
Power Input Voltage 100–240 V
Power Input Current 8.3 A Max
Operating Temperature Range 16°C to 40°C
Storage Temperature Range −18°C to 60°C
Operating and Storage Humidity Range 10% to 90% (non-condensing relative humidity)
Operating Altitude To 2000 m
Water Ingress Non-immersion, protection for damp wipe only
Weight 63.4 kg
Dimensions (W,H,D) 66 cm × 53 cm × 74 cm
Installation Guide
The following section is included for reference purposes only. As standard practice, SGI-DNA will install
the BioXp™ System.
CAUTION: Read the entire Installation Guide before unpacking the BioXp™ System. Be sure to read and
adhere to the "Safety Warnings" on pages 4 and 5. Contact SGI-DNA immediately if you have any
concerns or questions.
System Location
The BioXp™ 3200 System has a compact footprint and is designed to be used in the typical laboratory
environment. Install the instrument in a location that meets the following requirements:
• Lab bench space that is 87 cm (35 inches) wide and 74 cm (29.2 inches) deep to accommodate the
instrument and allow for 10 cm of clearance on the sides for proper ventilation.
• Clearance of 79 cm (31 inches) above the lab bench to allow the door to open upward properly
• An available AC power outlet present within 2 meters of the instrument
• Available internet connection through a wired Ethernet connection

7
Setup Precautions
Place the instrument on a clean, dry, at surface capable of holding the
weight of the system.
Allow 10 cm of clearance on both sides of the instrument for proper
ventilation.
Make certain that the power cord connection point is free and clear of
obstructions so that it is easily accessible.
The intended location must be stable so that the instrument will not move
or vibrate excessively when in use.
Avoid dusty areas.
Avoid areas where the instrument would sit in direct sunlight or near a
heat source.
Do not set the instrument up where liquids or chemicals are used. Ensure
that no liquids are spilled into the instrument.

8
Unpacking, Set up, and Power Up
WARNING! Using the BioXp™ System in a manner not specied by SGI-DNA may result in damage to the
equipment and/or personal injury.
1. Remove the crate from the BioXp™ System by positioning two people across from each other. Carefully
lift the box upward while leaving the instrument stationed on the foam cushions on the pallet as
shown in the following illustrations:
2. Remove the foam packaging materials from the top of the instrument.
3. Carefully coordinate lifting the BioXp™ System o of the pallet with at least two people using proper
lifting technique:
4. Making certain the path is clear, carry the instrument and place it on the site prepared according to the
stipulations outlined in "System Location" on page 6.
5. After removing the power cord from packaging, connect it to the power inlet located on the right rear
side panel of the instrument.
6. Check that the power switch located above the power cord inlet is in the “o” position (0).
7. Connect the instrument to a grounded power outlet.
Note: We recommend connecting the instrument to a 1500 VA/900 W uninterruptible power supply.

9
Getting to Know the System
Hardware Overview
Figure 1. Front and side view of the BioXp™ 3200
System.
Figure 2. The BioXp™ 3200 System Deck.
Figure 3. Deck Map.
1– Heated Lid
2– Thermocycler
3– Purication Module
4– Thermal Cover
5– Reagent Chiller
6– Recovery Chiller
7– Reservoir Retainer
8– Strip Well Holder
9– Tip Tray Retainer 1
10– Tip Tray Retainer 2
11– Tip Tray Retainer 3
12– Tip Tray Retainer 4
13– Waste Bin
Instrument Ports and Power Switch
Location Label number Port/Inlet Used to
12345
1 USB Do not use
Note: The USB port is for instrument
diagnostics and is for authorized service
personnel use only.
2 Ethernet Connect to sgidna.com for system operation
3 Fuse Do not use
4 Power
switch
Switch power to the instrument on or o.
Note: We recommend leaving the
instrument on continuously.
5Power inlet Power the instrument
Figure 4. Power On/O switch and communications ports.

10
Starting the BioXp™ System
Ethernet Set Up
The BioXp™ System requires an internet connection. Prior to connecting the instrument to the internet, be sure to
test the connection. Connect the provided RJ45 Ethernet Cable to the Ethernet port located on the rear of the unit
to an available Ethernet wall jack.
Start the BioXp™ System
1. Turn the instrument on using the power switch located on
the side of the instrument.
The BioXp™ System will initiate a self-check process to verify the correct functionality of motion control
and other internal systems of the instrument. If the instrument is unable to perform a successful self-check
it will alert the user to the problem and will prevent the instrument from operating until the problem has
been addressed. The self-check process has been carefully developed to ensure that the BioXp™ System is
operating within optimal calibration ranges and that all systems are functioning correctly before initiating
a run.
2. After the self-check, one of the following screens is displayed:
If reagents from previous jobs are on the
instrument deck, a Remove Materials
Screen is displayed. Open the door,
remove the materials from previous jobs,
and then close the door.
If you are ready to load the instrument and
begin a run, refer to the appropriate deck
loading instructions for your system run.

11
Quick Start Guide: Performing an Instrument Run
After installing and setting up the BioXp™ System, the instrument is ready for operation. The following instructions are
intended for experienced users. If this is your rst time operating the BioXp™ System or if you are unfamiliar with operating
the instrument, refer to the detailed instructions on pages 23–29.
BioXp™ Tiles and Libraries Quick Start
The instructions on this page are specic for building BioXp™ Tiles and Libraries. See page 12–14 for instructions for
loading the instrument for building BioXp™ Clones.
Each BioXp™ Tiles kit includes Module A (+4°C) and Module B (−20°C). Refer to the Loading Map shipped with your BioXp™
Reagents for the most up-to-date loading instructions.
1. If the door is closed, select "Unlock Door" from the instrument LCD screen and open the door
2. Thaw the DNA Assembly Reagent Plate (at 25°C for 1 hour or on ice for at least 3 hours)
3. Load tips by aligning the tip tray notch with the upper left corner of each Tip Tray Retainer
Load 3 x 50 µL tips
Load 1 x 200 µL tips
4. Add a minimum of 12 mL freshly prepared 70% ethanol to the reusable Ethanol Reservoir
Load Ethanol Reservoir in the right-most Reservoir Retainer position of the instrument deck
Note: Do not discard the Ethanol Reservoir after the run; keep for future use
5. Load plates stored at 4°C:
Load the Recovery Plate onto the Recovery Chiller with the notch in the upper left corner
Load the Oligo Vault™ Plate so that the notch is positioned in the upper left corner of the Thermocycler
6. Briey spin the DNA Purication Strip
Load the black DNA Purication Strip into the #1 position (left-most) with the strip pinhole closest to the front
of the instrument
7. Secure strips with the spring-loaded arms while holding strips securely in place
8. Spin the thawed DNA Assembly Reagent Plate for 1 minute at 500 rpm. Visually inspect the wells to ensure that they
are completely thawed before loading the plate.
Load DNA Assembly Reagent Plate onto Reagent Chiller, notch in the lower left corner
Note: Be certain that the plate is properly seated within the chiller and that the barcode is on the right
9. Refer to the photo in the lower left panel below. Conrm that all components are securely seated. Close the door.
10. After the deck inspection, press Start Now or Delay Start (no more than 2 hours) to begin the run.
Loaded Deck at Beginning of Run Deck at Run Completion
Oligo Vault™
Thermal Cover DNA Assembly
Reagent Plate
Recovery
Plate
Ethanol
Reservoir
50 μL tips 50 μL tips
50 μL tips 200 μL tips
black strip
Oligo Vault™
Recovery Plate
Location of BioXp™ Tiles after the run
After the instrument run, BioXp™ nal products are located in Wells A1–H4 of the Recovery Plate within the Thermocycler.
BioXp™ Tiles and Libraries are provided in 45L TE Buer. The expected yield is >200 ng of puried, linear DNA. If you will not
be using the nal products immediately, seal the Recovery Plate and store at 2°C to 8°C for up to one week or at −20°C for up
to one year.

12
BioXp™ Cloning Quick Start
The following instructions are intended for experienced users only. For additional instructions, see:
• The BioXp™ Custom Cloning Vector Preparation Guide available at sgidna.com.
• Detailed loading instructions on pages 23–29.
Guidelines for preparing the BioXp™ custom vector strip
1. After you have prepped your vector according
to the protocols and guidelines in the BioXp™
Custom Cloning Vector Preparation Guide available
at sgidna.com, adjust the prepared vector
concentration according to the table:
Vector Size (kb) Concentration (ng/µL)
3–5 15–20
5–7 20–25
7–9 25–30
9–12 30–35
2. Determine the volume of prepared linear vector
you will add to wells A, C, E, and Gof a BioXp™
Vector strip.
Note: Volume recommendations are subject to
change. Please contact us at
[email protected] for more information.
Number of BioXp™ Cloning Reactions Volume/
well
≤16 Reactions 12 µL
>16 Reactions 18 µL
3. Add 12 or 18 µL of prepared linear vector to wells
A, C, E and G of a BioXp™ Vector strip. Do not seal
the strip. Ensure that no air bubbles have been
introduced and that the resuspended vector is
at the bottom of the strip wells. Load the lled
custom strip on the deck with the pinhole closest
to the front of the instrument. A C E G
B
D
F
H
pinhole
EXAMPLE: For 8 cloning reactions, adjust the volume of a 10 kb vector to a nal concentration of 30–35 ng/µL. Add 12 µL of
the linearized, prepared vector to the four strip wells (A, C, E and G).
Total amount of required vector = 1.44 to 1.68 µg.

13
BioXp™ Cloning Quick Start: Loading the instrument
Each BioXp™ Cloning kit includes Module A (+4°C), Module B (−20°C), and Module C (−20°C).
1. If the door is closed, select "Unlock Door" from the instrument touch screen and open the door
2. Thaw −20°C components as directed below:
• DNA Assembly Reagent Plate (at 25°C for 1 hour or on ice for at least 3 hours)
• GA Cloning Strip and Vector Strip (30 minutes on ice)
3. Load tips by aligning the tip tray notch with the upper left corner of each Tip Tray Retainer
Load 3 x 50 µL tips
Load 1 x 200 µL tips
4. Add a minimum of 12 mL freshly prepared 70% ethanol to the reusable Ethanol Reservoir
Load Ethanol Reservoir in the right-most Reservoir Retainer position of the instrument deck
Note: Do not discard the Ethanol Reservoir after the run; keep for future use
5. Load plates stored at 4°C:
Load the Recovery Plate onto the Recovery Chiller with the notch in the upper left corner
Load the Oligo Vault™ Plate into the Thermocycler with the notch in the upper left corner
6. Briey spin the strips. Visually inspect the wells to ensure that they are completely thawed. Load in the order listed
and shown below, with the strip pinhole closest to instrument front
Load the black DNA Purication Strip into position #1
Leave position #2 empty
Load the purple GA Cloning Strip into position #3
Load the red pUCGA 1.0 or Custom Vector Strip into position #4
7. Secure strips with spring-loaded arms while holding the strips in place.
8. Spin the thawed DNA Assembly Reagent Plate for 1 minute at 500 rpm.
Visually inspect the wells to ensure that they are completely thawed.
Load DNA Assembly Reagent Plate onto Reagent Chiller,
notch in the lower left corner and barcode on the right
Note: Be certain that the plate is properly seated within the chiller.
9. Refer to the photo in the lower left panel below. Conrm that components are securely seated. Close the door.
10. After the deck inspection ends, press Start Now or Delay Start (no more than 2 hours) to begin the run.
Loaded deck at beginning of run
Oligo Vault™
Thermal Cover
DNA Assembly
Reagent Plate Recovery
Plate
Ethanol
Reservoir
50 μL tips 50 μL tips
50 μL tips 200 μL tips
black strip
purple strip
red strip
or

14
After the cloning run: nal DNA product location
Deck at run completion
Recovery Plate Oligo Vault™
keep keep
keep
keep
keep
Items to keep
DNA product Located within Storage instructions
Cloning Reaction
(wells A1–H4) Recovery Plate
Seal and store at 2°C to 8°C for up to one week or at −20°C for up to one year.
Uncloned Tiles
(wells A5–H8)
Oligo Vault™Plate
(foil covered)
Ethanol Reservoir
(empty and rinse for next use)
Recommendations
After the BioXp™ run is complete, cloning reactions are ready for transformation. We recommend diluting cloning
reactions 1:2 with molecular biology grade water before transformation.
Analyze Tiles– We recommend evaluating the success of the assembly reaction by running a gel containing the
uncloned BioXp™ Tiles from the Oligo Vault™ Plate before transforming clones.
Transformation– We recommend using E. cloni 10G Chemically Competent Cells (LucigenCat.No.60107, free samples
available at Lucigen.com) or TransforMax™ EPI300™ Electrocompetent E. coli (LucigenCat.No.EC300110). If other cells
are used, use competent cells with a transformation eciency ≥1 × 109CFU/g pUC19.

15
Operational Features of the BioXp™ System
Delay Start
The Delay Start function is a useful tool enabling you to schedule instrument runs at your convenience.
Immediately after a Delay Start is scheduled (before the delay time period elapses), the instrument
initiates reagent mixing from the Reagent Strips and the Reagent Plate. Therefore, ensure that the
Reagent Strips and Reagent Plate have thawed completely before initiating a Delay Start. If you decide to
cancel a Delay Start, consider that you may need to replace the Reagent Strips and Reagent Plate and run
the job at a later date since the master mixes created from combining the contents of the Reagent Strips
and the Reagent Plate are thermolabile.
To perform a Delay Start:
1. After pressing Delay Start on the Job Initiation Screen, the system will display a
DelayTimerScreen:
2. Use the arrows to set the delay start time and press OK.
Note: We recommend using the Delay Start feature for short periods of time (less than 2 hours)
asnecessary.
3. After the delay time has been scheduled, the system will prepare reagents for the run. The system
displays a Delay Start Screen with a timer showing the length of time left until the run begins
(in hours : minutes : seconds) and the expected time of job completion (also in hours : minutes :
seconds):
4. After the system has prepared the reagents for the run, a new countdown screen is displayed. You
may opt to bypass the delay and start the run immediately by pressing Start Now. If no action is
taken, the instrument run will begin when the timer reaches 0:00.

16
Tracking Progress During a Run
Time to Completion
During a run, the instrument will display the projected time remaining for the run
(in hours : minutes : seconds) and the estimated Time of Completion, as shown in the following
illustration.
Ways to Track Progress
You can track the progress of your reaction in a number of ways:
Parameter Denition
Time to Completion The system estimates the time at which the run will be completed.
Time Remaining The system estimates the time remaining for completion.
Visual Progress The system provides a progress bar through the various steps to completion.
Note: The scale of each step is not linear. (i.e. Step 1 requires much more time
than Step 4 but both steps are each depicted with a similar sized time lapse
bar).
Color Indicators
The internal colored lights change during the run process. The colors indicate the status of the process
taking place. The background color of the screen changes to indicate the following:
Touchscreen
Background Color Indication
Blue Normal operation: run set up or run in progress
Yellow System check or prompt requiring user attention
Red Error message
Green Processing completed

17
Canceling a Job During Delay Start
To cancel a job after initiating a Delay Start, press Cancel Job .
The system will display a screen reminding you that materials may have already been compounded,
rendering reagents unusable at a future time.
Press To
NO (keep running) Continue with the delay start and
instrument run
YES (stop running) Cancel the delay start and abort
the job
Canceling a Job During a Run
IMPORTANT! You will not be able to reuse reagents if you cancel a job after the run has initiated and the
Reagent Plate Seal has been broken. Do not cancel a run unless absolutely necessary.
1. If you need to cancel a job during a run, slide
your nger to the right across the bar on the
bottom of the Display Screen during a Run.
Slide to cancel
2. After sliding to cancel, the system will display
a Conrmation To Cancel screen. Press YES
Cancel Job to end the run or No to continue
the run.
If you press YES Cancel Job, the instrument
will display a Canceling Job screen until the job
cancel is complete.
3. When prompted, remove all materials and
used or partially used consumables from the
instrument deck:
Shutting down the BioXp™ System
We recommend leaving the instrument on continuously. Only turn the instrument o when necessary,
such as when moving the instrument to another location. If the instrument must be turned o, toggle the
power switch located on the side of the instrument (near the power cord) to the OFF position.