Policies and Guidelines

These policies are put in place to keep the facility running smoothly, and to keep costs and downtime to a minimum. Please respect our policies. Please report to staff any issues that arise so that we can deal with them as soon as possible. We are here to help!

Biosafety and Safety Precautions
Communication
Starting Work at CEMC
Cancellation, Rescheduling, and Late Policy
Materials and Data
Authorship/Acknowledgement

Biosafety and Safety Precautions

EHS Safety Trainings

Below is a list of important Stanford EHS safety trainings depending on the type of work you will perform. More details can be found in the sections below.

Radiation (negative stain)–EHS-5250
Cryogen–EHS-2480
Compressed gas–EHS-2200
Bloodborne Pathogens–EHS-1600 (for BSL2 work)

Biosafety Level

BSL1-ONLY INSTRUMENTS

The following instruments are equipped for BSL1 samples ONLY (e.g. purified recombinant protein):

ChEM-H Glacios
Morgagni

See the note in “BSL2 PROJECTS AND RESTRICTIONS” for information on what samples are considered BSL2.

DEFINITIONS OF BSL2 AND INFECTIOUS AGENTS

BSL2–As per Santa Clara County and Stanford University, all human cells are considered BSL2, including commercially available cell lines normally labeled as BSL1 (e.g. HEK cells). Unmodified cells are considered “potentially infectious” and “Universal Precautions” must be taken when handling the material.

Universal precautions–Universal precautions assumes that all materials contain an infectious or harmful agent, regardless if explicity known/identified or not. See more about Universal Precautions in the next section.

Infectious agents (BSL2+)–Stanford University follows the categorizing of infectious agents as described in Biosafety in Microbiological and Biomedical Laboratories (BMBL), 6th Edition written by the Centers for Disease Control (CDC) and National Health Institutes (NIH). Please refer to the document for comprehensive information on what constitutes an infectious agent. A rule of thumb is that anything containing virus, infectious bacteria, or non-exempt nucleic acids is an infectious agent. Common transgenic vectors that fall into this category are lentivirus and CRISPR.

UNIVERSAL PRECAUTIONS

As the Fairchild (D045 and D047) and Building 006 at SLAC are designated BSL2 areas, “Universal Precautions” must be observed when working in those areas. Universal Precautions assumes that all materials may be infected with a transmissible agent. To observe Universal Precautions, one must take care when working in the area, including cleaning tools and surfaces with 10% bleach (preferred) or 70% ethanol, and wearing proper PPE. For more information, see the note in the “BSL2 PROJECTS AND RESTRICTIONS” section. When BSL2 is being done, the door to the room must remain closed; if the door is closed, assume BSL2 work is being conducted.

Proper PPE includes:

Goggles
Lab coat
Gloves

BSL2 PROJECTS AND RESTRICTIONS

At Stanford, all human cells are classified as BSL2, including HEK cells and other commercially available human cells normally listed as BSL1. Untreated/unmodified human cells are considered “potentially infectious” and “Universal precautions” need to be taken whenever handling BSL2 samples or working around them. This means properly decontaminating materials that come in contact with the sample with 10% bleach or 70% ethanol, and wearing proper PPE – lab coat, gloves, goggles.

See the “Steps to begin using BSL2 samples at CEMC” to get started. You will need to submit the BSL2 Questionnaire and receive approval from CEMC for each sample type before beginning BLS2.

BSL2 Questionnaire

For samples containing infectious agents, including genetic modifications (e.g. lentivirus transfections, CRISPR modifications, and non-exempt rDNA/synthetic nucleic acids)–Users need to have an IBC protocol before beginning such a project and adhere to the approved protocol for handling the samples. The CEMC workspace needs to be added to the protocol upon approval for use at CEMC before beginning work. See the EHS IBC website for more information. PERSONNEL WORKING WITH BSL2 SAMPLES MUST ADHERE TO PROTOCOLS AND RULES OR ELSE THEY WILL BE REPORTED TO EHS.

Contact Nneha regarding BSL2 samples at SLAC for TEM1 and TEM4 before beginning work to ensure that you are compliant with all of SLAC’s protocols and precautions (See the SLAC WPC for more information).

Violations of BSL2 procedures, or bringing in agents that deviate from the approved protocol, will result in disciplinary action through EHS, including but not limited to: Safety investigation, pause or revocation of BSL2 operations for the responsible lab, and retraining.

STEPS TO BEGIN USING BLS2 SAMPLES AT CEMC

Below is a comprehensive guide to the steps to obtaining permission for BLS2 work. These steps must be done on a per-sample-type basis.

Confirm whether your sample is BSL2. Visit the EHS IBC website and consult with EHS/IBC with questions about the sample.
Identify the hazards and the inactivation procedure (clean-up) for your sample.
Determine if your sample contains potentially infectious agents and create an IBC protocol. Consult with EHS/IBC with any questions.
Fill out the BSL2 Questionnaire and have you and your PI sign the form.
Send the form to stanford-cemc@stanford.edu to review. DO NOT begin work until CEMC has approved the sample.
Once accepted for use at CEMC, if your sample contains a potentially infectious agent, add Fairchild D047 and D045 to your IBC protocol workroom list. Send a PDF copy of your updated IBC protocol to stanford-cemc@stanford.edu.
Adhere to all safety rules and responsibilities for working with the sample. Make sure you have completed all required EHS trainings before beginning work.

RESPONSIBILITIES OF BSL2 USERS

Users must take EHS-1600-Bloodborne Pathogens before beginning BSL2 work.
BSL2 work will be performed by the user ONLY. Staff will have limited ability to intervene with BSL2 samples.
Users must make sure that they have the proper training and documentation before beginning BSL2 work (e.g. IBC protocols, BSL2 Review Form).
Users are responsible for making sure that they follow the BSL2 protocols as mandated by the IBC for their particular sample, and that they are compliant with all rules and regulations.
It is the user’s responsibility to clean up and decontaminate the equipment before and after use and to properly dispose of biohazard waste in the biohazard waste bin. It is the user’s responsibility to make sure that they are compliant with all rules and regulations.

Radiation

CEMC has a designated negative staining section in Room D047 of Fairchild. We use uranyl acetate/formate for negative stain. Standard uranium (238) is very mildly radioactive, emitting alpha particles that are easily blocked by gloves and the outer layer of dead skin. Uranium-238 is most dangerous if ingested, and relatively safe otherwise. Users should not feel alarmed working within or around the radiation area. However, users should exercise caution and adhere to the radiation procedures by EHS. Dispose of anything that touched uranium in the radioactive waste bin. As we can only throw away solid waste, liquid waste needs to be absorbed onto a filter paper prior to disposal. DO NOT dispose of any other radioactive substance into our waste other than U-238. Users planning on working with radioactive materials (including U-238) need to take EHS-5250 Radiation Safety prior to using materials.

Waste

CEMC DOES NOT have chemical or hazardous waste disposal (exception: radioactive waste from Uranium-238. PLEASE NOTE: only U-238 may be disposed in our radiation waste container). Therefore, you must remove your own chemical or hazardous waste from the center and dispose at your own lab.

Signage

Please adhere to any posted signage around the facility, which will provide information on what cautions you should take, what to do in emergencies, and who to contact during emergencies.

Cryogens and Compressed Gas

This facility uses the cryogens liquid nitrogen (LN2) and liquid ethane. Users need to take EHS-2480 Cryogenic Liquids and Dry Ice Safety training prior to working with cryogens. Cryogens pose burn risk if contacted with skin. Liquid ethane can penetrate skin as well, causing instaneous subdermal injury. Always wear the proper PPE when handling cryogens – i.e., gloves, cryo-gloves, goggles, face mask, and long-sleeves and pants (lab coat prefered).

Additionally, both LN2 and liquid ethane can evaporate and rapidly displace oxygen, causing a suffocation hazard. Users should also take EHS-2200 Compressed Gas training. Ethane gas is also highly flammable so DO NOT let ethane gas escape into the room. Users need to undergo training with the staff before using ethane, which is only for the plunge-freezing process. Ethane training will be covered in the plunge-freezing training.

To dispose of LN2, place small amounts in the fume hood (such as vitrobot ethane cups). Empty large amounts of LN2, as from a 4L Dewar, into the storage Dewars or a styrofoam container large enough to accomodate the volume. DO NOT dump on the floor, as the floors are not rated for LN2.

For ethane, place the ethane cups in the fume hood.

Patient Data Statement

We are NOT equipped to handle HIPAA- or patient-protected data.

Communication

We use Slack for most of our communication, especially rapid communication. Please check the individual channels for the most up-to-date information regarding the facility. You can directly message staff on Slack as well for the quickest communication. If you do not have access to the CEMC slack group or any of the channels, please contact a CEMC staff member to add you.

Users should also join our email list serv to receive information on long-term updates, such as facility shutdowns (e.g. Winter Closure).

The Updates page of this website will also contain announcements such as closures, instrument downtime, and events.

You may also email any staff or the manager for any other concerns. See our “about us” page for contact details.

Starting Work at CEMC

General User Agreement

This user agreement appears when you sign up for iLabs and must be signed on iLabs before using the facility. A copy is shown here for reference.

User Agreement

Booking Instrument Time

Instrument booking and billing is handled on iLabs. For new users, please set up an iLabs account, then request training. Include the instruments you would like training on and what times you are available for training in the request.

Rules for booking:

Users can book up to 4 weeks (28 days) in advanced (all instruments).
For Aquilos, Krios, and Glacios: Limited 3 days per user per 4-week period unless permitted by staff (contact staff).
For Aquilos only: maximum 2 consecutive days per user per 4-week period.

Please also read the Cancellation policies below.

ALL new users must go through the training/vetting process (see below) before using instruments and equipment.

Training/Vetting

Training is requested through ilabs.

It is important that we ensure all new users know our policies and protocols. This includes users with prior experience. Those with prior may or may not be familiar with our setup, our exact instruments, or our policies, and this training/vetting process ensures we are all on the same page. For those with prior experience, the “training” session will act as a “vetting” session, whereby the user demonstrates their skill and staff will fill in the blanks where needed. Therefore, for those with ample prior experience, the vetting process will be quicker than full-on training.

PRE-TRAINING DOCUMENTS

Please review all documents that the staff request prior to your training session. This includes the protocols for each instrument. Users are advised to take their own notes during the training.

A great open-access source for learning about cryo-EM are the Grant Jensen Cryo-EM Lessons (“Cryo-EM University”)

User Level Definitions and Project Types

Users are categorized into 3 categories:

Trainee: User is undergoing the training/vetting process.
Basic user: User has been trained and is cleared to book instruments. User is semi-independent – still learning how to the use the instruments but is capable of operating the instrument with assistance from staff from time-to-time. User cannot book instruments outside of working hours (9 am to 5 pm Mo-Fr).
Superuser: User can work independently on the instrument with little staff assistance (usually for more difficult, nontrivial problems). User can book instruments outside of working hours. Superusers have also demonstrated an excellent sense of responsibility for their actions and the facility. Superuser status is obtained at the discretion of the staff.

In addition to training, CEMC offers two other service types for projects:

Full Service: We will do everything from freezing the sample to obtaining data. User needs to provide the biochemical material.
Collaboration: We will do a full service and also process the data. Since data processing requires much more intellectual resources from our staff, the staff member should be an author on the paper (see Authorship below)

We are unable to do labwork or sample prep prior to the plunge freezing phase. Therefore, samples need to be provided in the final state prior to plunge freezing.

Cancellation, Rescheduling, and Late Policy

Cancellation

Please communicate on Slack to the instrument channels when you need to cancel a session, and contact staff to cancel the session.

Because of the high demand for the Aquilos and Krios instruments:

Sessions cancelled within 48 hours of the start of the scheduled time will be charged 100% of the session cost, unless the user can find someone to take the spot. For Monday, cancellation needs to be before the prior Friday.

For Glacios:

Sessions cancelled within 24 hours prior to the start of the scheduled time will be charged 100% of the session cost, unless the user can find someone to take the spot. For Monday, cancellation needs to be before the prior Friday.

**These penalties apply to all sessions (including training), unless the user is permitted to cancel after communication with Staff.

**When an instrument goes down, the above cancellation penalties do not apply. Users may then reschedule their sessions as detailed below.

Rescheduling

INSTRUMENT DOWNTIME

There are several circumstances that result in a session having to be rescheduled. CEMC will try to mitigate the impacts as best as we can. Many of the instruments will need repairs at unpredictable times. When an instrument needs to be repaired, the impacted users will need to be rescheduled. Impacted users will be given priority for the next available slot.

STAFF-INITIATED RESCHEDULING

In the rare event that a staff member needs to reschedule an appointment, they will notify the user as soon as possible. Staff will work with the user to reschedule. Users will not be charged for the missed session.

USER-INITIATED RESCHEDULING

If a user needs to reschedule due to circumstances not caused by the Center, the above cancellation policies will apply. The user can then reschedule at the first available slot.

Late policy

Users are charged at the start of their session, regardless if they are on time or late, unless otherwise waived at the discretion of the staff. Staff can also determine whether the session’s time may be adjusted or rescheduled to make up for the tardiness. Users must finish their session before the end of their scheduled time. If working with a staff member, please notify that staff member of the tardiness as soon as possible.

Materials and Data

Storage

We can only guarantee storage of materials and data for up to 30 days, at which point CEMC will dispose of the material at our discretion. Anything that is not properly labeled will be disposed of at our discretion after attempting to track down the owner; if the owner cannot be identified it will be disposed. We are not responsible for anything left at the facility.

We offer puck storage (preferred) or Falcon storage for grids. For information on puck storage at CEMC, see our puck manual. Falcon tubes must be labeled with a date of storage, name, lab, and grid info. Grids for the Krios microscopes may be stored in Dewar 10 at SLAC in Falcon tubes, labeled as detailed above.

Data drives may need to be purged sooner than 30 days if the storage drives are getting full. We will warn users about a data purge in advance. Fairchild Glacios and Morgagni data will automatically be purged after 30 days of acquisition (after new storage system is implemented).

TEM1 has a small storage drive and requires data purges usually within 3 days. Users must transfer their data within a day of acquiring and then notify the staff once the data has been transferred. The user or staff will then delete the data.

Use of data, data ownership, and responsibility

All data are intended for research use only and are not intended for human or animal medical diagnosis.

Data belongs to the researcher. Researchers are responsible for obtaining and storing their data files. Data can only be stored on our servers for 30 days before the Service Center can delete data.

No liability

All data and materials are provided as a service to the scientific research community. The Services are provided on an “as is” and “as available” basis. Service Center makes no representations and extends no warranties of any kind, express or implied. User hereby acknowledges that the Services are experimental and exploratory and that no particular results or outcome can be guaranteed. User also acknowledges that changing the scope of work may impact the cost of work.

Authorship/Acknowledgement

As per the policy of the Office of the Senior Associate Dean for Research at Stanford Medicine, if data obtained from the Service Center’s resources is used in a publication, the Service Center must be acknowledged [“Stanford Cryo-EM Center (cEMc)”]. Additionally, if Service Center personnel contribute intellectual resources to the work (including, but not limited to, data interpretation, experimental design, and manuscript preparation outside the Materials and Methods section), the personnel should be listed as a co-author on the publication. Authorship does not exclude payment of charges accrued for the work, as the materials and personnel time must be compensated.

Importance: Publications are an important metric for a Service Center’s impact, and publications help secure financial support from Stanford. Authorship/acknowledgement of the core lab is crucial in supporting ongoing shared resource operations and development, as well as in acquiring future instrumentation and capabilities. The Service Center is staffed by professional scientists and deserve recognition for their efforts. Proper authorship further supports the Service Center’s personnel in their careers.
Assistance: Service center scientists are available to assist with technical content, review, and method write-ups.
Guidelines: ABRF Recommended Guidelines for Authorship on Manuscripts provides further guidelines regarding authorship and acknowledgements.