USER HANDBOOK

BioFoundry Facility Guidelines, Laboratory Safety Plan, Training Guide & Lone Worker Policy

Access requirements, operational expectations, biosafety practices, and emergency procedures for the BSL-2 Knight Campus BioFoundry facility.

Table of Contents

1. Purpose and Scope     

2. Definitions and Abbreviations 

3. Area Configuration     

4. Training, Access and Authorization      

5. Personal Protective Equipment (PPE)   

6. Facility Entry and Exit Procedures        

7. Biosafety Practices     

8. Biological Materials and Approval Levels          

9. Chemical Handling     

10. Tool and Equipment Use       

11. Waste Management and Decontamination     

12. Housekeeping and Laboratory Etiquette         

13. After-Hours Use and Lone Worker Policy        

14. Training, Records, and Documentation           

15. Enforcement            

16. Violations and Enforcement

17. Revision History       

This document outlines access requirements, operational expectations, biosafety practices, and emergency procedures for the BSL-2 BioFoundry facility. The facility supports biological sample characterization, analytical assays, and associated instrumentation under Biosafety Level 2 containment.

These guidelines apply to faculty, students, staff, visiting scientists, and industry partners. All work must comply with University Environmental Health & Safety (EHS), Institutional Biosafety Committee (IBC), CDC/NIH BMBL guidance, and applicable federal, state, and local regulations.

Key terms and abbreviations used in this handbook.

The BioFoundry is organized into functional areas designed to maintain biosafety, optimize workflow, and protect shared equipment and biological materials.

Bio Characterization Area (Rooms 115, 115B, 115D)

Dedicated to the imaging, analysis, and characterization of biological samples, live cells, microorganisms, biomaterials, and engineered constructs using specialized BioFoundry instrumentation.

Permitted activities:

• Microscopy and imaging of fixed and live biological samples, including live-cell imaging
• Biochemical, molecular, and cell-based assays
• Biomaterial and engineered construct characterization
• Mechanobiology and mechanical testing of biological samples, cells, tissues, and biomaterials
• Live-cell experiments using approved equipment and appropriate containment procedures
• Analysis of fixed or inactivated bacterial and yeast samples
• Culture and analysis of approved live microorganisms in designated areas and equipment

Microbial Work

Live bacterial and yeast cultures may only be handled in designated BioFoundry spaces, including Room 115C, and using approved equipment and procedures. Microbial work must follow applicable BSL-2 practices and BioFoundry requirements. Users must receive approval and any required training before beginning live microbial work.

Live Cell Incubation Area (Room 117A)

Maintains and incubates viable cell cultures under controlled conditions. Supports CO₂ incubators and culture storage systems.

Permitted activities:

• Incubation and storage of actively growing mammalian or low-contamination-risk cell cultures
• Temporary placement of culture plates, flasks, or vessels in incubators
• Routine maintenance (e.g., medium exchange)
• Visual monitoring using an inverted microscope
• Short-term handling to maintain cell viability

Live Cell Manipulation Area (Rooms 117 & 119)

Dedicated to sterile handling and experimental manipulation of viable cells.

Permitted activities:

• During quarantine, routine cell culture procedures (passaging, plating, and expansion) may be performed before cells are transferred to the Incubation Area.
• Genetic manipulation (transfection, viral vector work, if approved)
• Sterile preparation of cultures
• Cell sorting and preparation for cytometry workflows
• Live-cell imaging and assays requiring viable cells
• Experimental manipulation with biomaterials or devices

Shared Support Area (Room 121)

Provides general laboratory resources and infrastructure.

Permitted activities:

• Storage of reagents in shared refrigerators/freezers
• Organization of glassware and laboratory supplies
• Access to shared equipment (autoclaves, etc.)
• Preparation of general laboratory materials

Note: This area is not for active experimental manipulation of biological materials.

Required Training to Use Facility

* Register for trainings here: https://uomytrack.pageuppeople.com/

NEMO Account

A NEMO account is required for scheduling training and equipment, logging usage, checking out consumables, and tracking service activities.

• NEMO – KC Cores: https://nemo.uoregon.edu
• NEMO – User Account Setup: https://knightcampus.uoregon.edu/facilities/core-facilities/user
• Using equipment without recording the session is prohibited.
• All users must scan into the NEMO kiosk upon entering the lab.
• All users must complete required institutional training prior to access.

Authorization

Users must be approved by BioFoundry Staff or the Core Facilities Director to gain access to BioFoundry. This authorization is required for all individuals entering the BioFoundry, including visitors or personnel who are only accompanying lab members and not performing experiments.

Visitor Policy

• Pre-approved by staff and always escorted.
• Visitors may not use equipment or handle chemicals.

Building Policy

• All users must follow Knight Campus building policies.

Minimum PPE

• Fully closed-toe shoes
• Long pants or equivalent coverage
• Laboratory coat (fluid-resistant required)
  • Bio Characterization — white coat (Rooms 115, 115B, and 115D)
  • Microbe room — disposable coat (Room 115C)
  • Cell incubation and manipulation — blue coat (Rooms 117, 117A, and 119)
• Safety glasses or goggles

Task-Dependent PPE

• Face shields or splash goggles
• Double-gloving
• Disposable sleeve covers
• Respiratory protection (fit-tested if approved)

Remove PPE before leaving the lab; follow facility disposal/storage procedures.

Any sign of contamination on lab coats (e.g., splashes, contact with contaminated areas, or getting wet) requires immediate replacement. Place the contaminated lab coat in the designated container for laundering. If a visitor borrowed a lab coat, ensure it is placed in the laundry bin after use. Change lab coats according to the specific area requirements to maintain biosafety.

Moving Between Laboratory Areas

To prevent cross-contamination between spaces:

• Lab coats must be changed/swapped when moving between the Characterization Bay (white lab coat) and the Live Cell Manipulation or Incubation bays (blue lab coat).
• Gloves must be removed before touching door handles, phones, or personal devices.
• PPE must never be worn outside of designated laboratory areas.

• Sanitize hands upon entry and before exiting.
• No food, drink, gum, cosmetics, or personal items.
• Clean and disinfect work surfaces before and after use using an approved disinfectant:
  • 70% ethanol: Apply enough to thoroughly wet the surface and allow the surface to remain wet for at least 1 minute before air drying.
  • PREempt Plus: Use according to the manufacturer’s instructions and required contact time for the intended application.
  • 10% bleach: Use when required for biological decontamination or specific procedures. Allow the appropriate contact time for the material being decontaminated, then remove bleach residue as needed to prevent surface damage or corrosion.
• Only approved materials may enter or leave the facility.
• Use the adhesive sticky mat at the laboratory entrance to remove dust and debris from footwear.
• Ensure proper use of PPE.

• Aerosol-generating procedures must be performed in certified Class II BSC.
• Minimize sharps; dispose of in labeled sharps containers.
• Follow all BSL-specific safety rules.
• Users are responsible for properly washing and decontaminating all materials and equipment used during their work.

Removing Biological Materials from the Facility

Biological materials may not be removed from BioFoundry without prior approval from BioFoundry staff. Before removal, materials must be placed in a closed, leak-proof primary container and transported in an appropriate closed, leak-proof secondary container. Materials must be properly labeled with their contents and any applicable biological hazard information. Additional packaging or transport requirements may apply depending on the type of biological material and its destination.

Contact BioFoundry staff before removing biological materials from the facility if you are unsure of the applicable requirements.

Liquid Biohazard Waste

Users are responsible for the proper disposal of liquid biohazard waste. Whenever possible, liquid waste must be collected and chemically inactivated in the room where it is generated to minimize the transport of untreated biological waste between laboratory areas.

Liquid biohazard waste must be carefully transferred into the designated, labeled liquid biohazard waste container containing the required concentration of bleach. Waste should be added slowly and as close to the container opening as it is practical to minimize splashing and aerosol generation. The appropriate bleach concentration and required contact time must be maintained before final disposal.

If untreated liquid biohazard waste must be transported to another room for disposal, it must first be placed in a closed, leak-proof primary container and transported within a closed, leak-proof secondary container. Open containers of untreated liquid biohazard waste must not be carried between rooms.

Liquid biological waste must be chemically disinfected with a final concentration of 10% bleach for at least 30 minutes. After the required contact time, the decontaminated liquid may be disposed of in the sink with running water, unless otherwise instructed by BioFoundry staff.

Cell Culture Best Practices

• Plan experiments and prepare all required materials before beginning work in the BSC.
• Disinfect all supplies and materials immediately before placing them inside the BSC and again before removing them from the BSC.
• Clean and disinfect BSC work surfaces before and after each use using the appropriate facility-approved disinfectant — 70% ethanol, PREempt Plus, or 10% bleach, as appropriate for the biological material and procedure. Follow the required contact time for the selected disinfectant.
• For work involving human-derived cells, blood, or other potentially infectious human materials, use PREempt Plus or 10% bleach, as appropriate, rather than relying solely on 70% ethanol. Follow the manufacturer-specified or facility-approved contact time.
• 70% ethanol may be used for routine surface disinfection when appropriate for the biological material and procedure.
• When 10% bleach is used, remove residual bleach from equipment surfaces after the required contact time, as appropriate, to minimize corrosion or surface damage.
• UV irradiation, when available and used, is considered a supplemental decontamination measure only and must not replace chemical surface disinfection.
• Work in an organized and deliberate manner. Avoid talking, coughing, rapid arm movements, or other activities that may disrupt airflow within the BSC.
• Keep only essential materials inside the BSC to maintain proper airflow and reduce contamination risk.

Materials Returning to Incubators and Fridges

• Clearly label containers with: user name, date, cell line/type.
• Opened reagents, media, and other materials used for cell incubation must remain within the BioFoundry to reduce risk of contamination.
• Ensure lids and caps are securely closed.

Incubator Guidelines

• Minimize door opening time.
• Label assigned lockers/compartments.
• Avoid placing uncleaned or external materials in the incubators.
• Report contamination, spills, odors, or unexpected changes immediately.

Consumables Tracking

• Use the NEMO system for all consumables check-out (tips, plates, flasks, lockers).
• Consumables that must be tracked are those sold by BioFoundry, including flasks, culture plates, pipettes, tips, bottles, and filters. A detailed list of available items will be provided. These paid consumables are stored in a dedicated cabinet designated exclusively for BioFoundry inventory.
• Failure to track consumables may result in restricted facility access or retraining requirements.

Shared Responsibility

• Leave the workspace equal to or better than you find it.
• Clean benches and common areas after use.
• Properly dispose of waste.
• Report dirty/abnormal equipment or abandoned materials.

Mandatory Core Equipment Training

All users must complete the BioFoundry Orientation before receiving independent access to the facility or using BioFoundry equipment. The orientation covers facility organization, PPE requirements, biosafety practices, waste disposal, emergency procedures, access policies, and general laboratory expectations.

Following orientation, equipment access is organized into training levels based on operational complexity, safety considerations, and the level of independent use permitted.

• Level 0 – BioFoundry Orientation
  Required for all BioFoundry users. Completion of the orientation provides general facility access but does not automatically authorize use of specialized equipment, cell culture areas, or restricted activities.
• Level 1 – Routine Laboratory Equipment
  Includes standard laboratory equipment that can generally be used following BioFoundry Orientation and basic operating instructions. Examples include centrifuges, balances, water baths, and other routine laboratory equipment. Instrument-specific training may not be required unless otherwise indicated.
• Level 2 – Specialized Equipment
  Includes instruments that require additional operating knowledge but may or may not require formal instrument-specific training, depending on the user's experience and intended application. Examples include routine fluorescence microscopes, such as the ECHO, cryostats, plate readers, and similar equipment. BioFoundry staff may require training or demonstration of proficiency before independent use.
• Level 3 – Cell Culture and Advanced Instrumentation
  Requires instrument- or application-specific training and demonstrated proficiency before independent use. This level includes cell culture activities and specialized instrumentation such as flow cytometers, advanced microscopy systems, rheometers, DMA and other mechanical testing instruments, Seahorse analyzers, and similar advanced platforms.

Additional training or approval may be required for advanced applications, specialized accessories, live-cell experiments, biological materials requiring additional containment, or procedures involving increased biological or operational risk.

Users may only operate equipment and perform activities for which they have been trained and authorized. Unauthorized use, use beyond the user's approved training level, or failure to follow BioFoundry procedures may result in suspension or loss of equipment and/or facility access.

Proper Material Labeling

• Username / lab
• Date
• Cell/reagent/sample identity
• Expiration
• Notes

Improperly labeled materials must not return to storage/incubators.

The BioFoundry is designed to support a broad range of biological and bioengineered materials while maintaining a safe shared laboratory environment and minimizing the risk of exposure and cross-contamination.

Biological materials are classified into four approval levels based on their biosafety requirements, contamination potential, experimental procedures, and potential impact on other users and shared equipment.

Users are responsible for accurately identifying the biological materials used in their experiments and informing BioFoundry staff whenever a new biological material or organism is introduced.

Level 1 – Routine Use: No Additional BioFoundry Approval Required

Routine, low-risk biological materials may be used without additional BioFoundry pre-approval after the user has completed the required BioFoundry orientation and applicable instrument training.

Examples include:

• Established, low-risk mammalian cell lines appropriate for standard BSL-2 laboratory practices
• Non-infectious engineered mammalian cell lines covered by applicable institutional approvals
• Fixed or appropriately inactivated biological samples
• Sterile biomaterials and non-biological samples
• Other biological materials determined to present minimal additional contamination or exposure risk

Users must follow all BioFoundry SOPs, PPE requirements, room-use restrictions, waste disposal procedures, and decontamination requirements.

Level 2 – BioFoundry Pre-Approval Required

Biological materials that present an increased risk of environmental or equipment contamination require approval from BioFoundry staff before use.

Examples include:

• Bacteria
• Yeast
• Other low-risk microorganisms
• Approved genetically modified microorganisms
• Experiments combining microorganisms with mammalian cells or biomaterials
• Live microbial samples intended for analysis on shared BioFoundry equipment

Routine cultivation and manipulation of approved bacteria and yeast must be performed in the designated Microbe Area (Room 115C) unless another location has been specifically approved.

Approved microorganisms may be used on selected shared instruments outside Room 115C, including equipment such as the Seahorse XF Pro or compatible imaging and characterization systems, only when the specific experiment has been reviewed and approved in advance by BioFoundry staff.

Approval may include requirements for sample containment and transport, instrument protection, scheduling, cleaning and decontamination, or staff supervision.

Level 3 – BioFoundry Pre-Approval Required and Special SOP

Materials presenting additional biological, exposure, or regulatory risks require review before they are brought into or used within BioFoundry.

Examples include:

• Human blood or blood-derived materials
• Primary human tissues, cells, or other human specimens with potential exposure risks
• Potentially infectious human or animal materials
• Viral vectors or viral systems requiring additional biosafety controls
• Microorganisms with clinically relevant antibiotic resistance or other enhanced risk characteristics
• Genetically modified organisms requiring additional institutional oversight
• Biological toxins or other biologically active hazardous materials
• Primary animal specimens presenting potential biological hazards
• Environmental, clinical, or other samples with incompletely characterized biological risks

Depending on the material and experiment, authorization may require an approved experimental SOP, documentation of biological hazards, specialized training, exposure-response procedures, or additional containment and decontamination measures.

Approval of biological material does not automatically authorize its use on every BioFoundry instrument. Instrument-specific approval may be required when an experiment could expose shared equipment, laboratory spaces, or other users to biological material.

Level 4 – Not Permitted / Outside BioFoundry Scope

Some biological activities are not appropriate for routine work within the BioFoundry.

This includes:

• Work requiring containment above BSL-2
• Work with biological agents for which the BioFoundry does not have appropriate containment, equipment, procedures, or training
• Materials whose biological hazards cannot be adequately identified or controlled
• Experiments presenting an unacceptable exposure or cross-contamination risk to other users or shared equipment
• Any biological activity determined by BioFoundry, EHS, IBC, or other institutional safety authorities to be incompatible with the facility

BioFoundry staff may determine that additional institutional review is necessary before deciding whether a proposed activity can be accommodated.

PI approval alone does not constitute BioFoundry authorization for Level 2, Level 3, or Level 4 activities.

General Requirements

All users must:

• Use biological materials only in approved laboratory areas.
• Follow applicable University of Oregon biosafety requirements and BioFoundry SOPs.
• Use appropriate PPE and follow room-specific PPE requirements.
• Transport biological materials between rooms using appropriate secondary containment.
• Follow approved cleaning and decontamination procedures after each experiment.
• Properly dispose of biological and sharps waste.
• Immediately report spills, exposures, contamination events, or unexpected biological hazards.
• Notify BioFoundry staff before introducing a new organism, cell type, biological agent, or experimental condition when its approval level is uncertain.

When in doubt, contact BioFoundry staff before beginning the experiment.

The purpose of this approval system is to enable the BioFoundry to safely support a broad range of biological research while protecting users, shared equipment, laboratory spaces, and other ongoing experiments.

• Follow all Standard Operating Procedures (SOPs) and wear appropriate PPE.
• Follow and abide by the University of Oregon Chemical Hygiene Plan: https://safety.uoregon.edu/sites/default/files/2023-10/chemical-hygiene…
• Get help if you’re uncertain how to work with a particular chemical.
• Perform chemical work only at designated hoods/benches.
• Label all containers with full chemical name, user name, and date.
• Use secondary containment for all liquid chemicals.
• Dispose of waste in clearly labeled waste containers.
• Never mix chemicals unless the procedure specifically calls for it.
• A buddy system is required for work with dangerous chemicals or after-hours use.

All equipment in the BioFoundry is shared and requires proper training before use.

General Rules

• Users may only operate equipment for which they have completed training.
• Equipment must be reserved and logged through the scheduling system – NEMO.
• Equipment must be left clean and ready for the next user.
• Equipment problems or abnormal behavior must be reported immediately.

Training Levels

BioFoundry users must complete the training applicable to the activities and equipment they intend to use.

• BioFoundry Orientation — Required for all new BioFoundry users. This orientation covers general facility rules, laboratory safety, access procedures, designated work areas, waste management, and emergency procedures. Required BioFoundry PPE will be provided, and its proper use will be reviewed during the orientation.
• Equipment Training — Required before independent use of BioFoundry instruments and equipment. Training is instrument-specific and may include equipment principles and operation, startup and shutdown procedures, routine user maintenance, basic experimental workflows, and applicable safety requirements. Additional training may be required for specialized or non-routine applications.
• Cell Culture Training — Required for users who will perform cell culture activities in the BioFoundry. Training covers BioFoundry-specific cell culture practices, aseptic technique, use of biosafety cabinets, contamination prevention, incubator use, cell culture workflow, disinfection, and biological waste handling.

Completion of BioFoundry Orientation does not automatically authorize independent use of equipment or cell culture areas. Users must complete the applicable training and demonstrate proficiency before independent operation.

• Solid biohazard waste must be disposed of in designated red biohazard bags.
• Sharps must be disposed of immediately in approved sharps containers.
• Autoclaves must not be used for the decontamination of potentially infectious materials unless the autoclave is maintained and tested in accordance with applicable Oregon Health Authority requirements.
• Autoclave use is restricted to trained and authorized users.
• Liquid biological waste must be chemically disinfected using a final concentration of 10% bleach for a minimum contact time of 30 minutes before disposal.
• Liquid waste should be handled carefully during collection and treatment to minimize splashing and aerosol generation.

Important: Liquid Waste and Tip Disposal

• All disposal of liquids and pipette tips containing liquid that are handled inside a Biosafety Cabinet (BSC) must first be discarded into a pre-decontamination container containing bleach at a final concentration equivalent to 10% of the total volume.
• Liquid waste and pipette tips should be poured through a funnel equipped with a mesh strainer. The liquid fraction must pass through the strainer and be collected in the designated main liquid biohazard waste container containing bleach to ensure proper chemical inactivation. The retained pipette tips must then be disposed of in the appropriate solid biohazard waste container.

• Keep workspaces clean and organized.
• Store materials in designated refrigerators and freezers.
• Clearly label all storage containers.
• Minimize noise and disruptions in shared spaces.
• Report unsafe or unsanitary conditions immediately.

BioFoundry allows work outside normal hours, but users must evaluate safety before starting. New or recently trained users are encouraged to begin experiments before 3:00 PM so staff can assist with setup, operation, shutdown, and troubleshooting.

After-hours work may occur without staff present; in this case, the user and their PI assume full responsibility for experiment safety and equipment use. Users must follow all University of Oregon EHS policies regarding working alone. High-risk activities — such as handling hazardous chemicals, high-energy equipment, lasers, or biological hazards — should not be performed alone.

Manipulation of live cell cultures after hours is strongly discouraged; if necessary, the user and PI accept responsibility for associated risks. Users must ensure that after-hours work does not compromise personal safety, lab safety, equipment integrity, or University policy compliance.

Permitted Activities (with PI Approval)

• Data analysis and computer work
• Operation of non-hazardous instruments
• Handling of fixed, inactivated, or non-infectious samples
• Manipulation of cell cultures and use of equipment for which the user has been trained

Activities We Strongly Discourage

• Handling infectious materials
• Procedures generating aerosols
• Use of sharps with biological materials
• Biological spill response or biosafety cabinet maintenance

Lab users are able to handle small spills both inside and outside the BSC, as covered in the UO Biological Safety Manual: https://safety.uoregon.edu/lab-research/biosafety

Buddy System

• High-risk or after-hours work requires a buddy system or check-in procedure.
• Users must inform colleagues before beginning work.
• Check-ins via phone, text, or safety application may be required for lower-risk activities.
• A buddy must be able to see you and assist in person when high-risk activities are being performed after hours or on weekends.
• Working alone and/or after hours in BSL-2 laboratories is discouraged due to safety risks. See documentation attached.

• All training must be completed before facility access is granted.
• Training records must be maintained and updated annually.
• Documentation for SOPs, LSPs, and equipment training must be retained.

• Noncompliance may result in retraining or suspension of facility access.
• Serious violations may be reported to the PI, IBC, and EHS.

Failure to follow any BioFoundry guideline may result in:

• Verbal or written warnings
• Temporary suspension of access
• Permanent removal from BioFoundry privileges

Major safety violations will be reported to department leadership and University EH&S.

The BioFoundry is a shared, regulated BSL-2 facility. Every user shares responsibility for keeping it safe, compliant, and ready for the next person.

Protect yourself and your samples by leaving the BioFoundry better than you found it.