S2C2 Project-tailored cryoEM Training Program

Program Objective

The S2C2 Project-tailored cryoEM Training Program provides training in cryo-specimen preparation, grid screening, and data collection.  This protect-tailored cryoEM training program is offered to individuals who would like to become more familiar with cryoEM single particle analysis (cryoEM SPA), high-resolution cryogenic electron tomography (cryoET), or cryogenic electron diffraction (cryoED) workflows, improve their cryoEM skills, and focus on a biospecimen of their choice.  This program is best suited for scientists deep in their own research who are having difficulty with cryoEM SPA, cryoET, or cryoED of their biospecimen(s).  The curriculum will folllow the traditional cryoEM workflows, but training will be tailored for the trainee's samples and skill/experience level.  Our goal is to help trainees become confident and proficient in cryoEM workflows especially cryo-specimen preparation.  This program can be conducted remotely.

Why should you apply?

  • To learn the vitrification method(s) to prepare cryo-specimens.
  • To optimize cryo-specimen preparation of a new biospecimen.
  • To overcome challenges in preparing cryo-specimens for high-resolution studies.
  • To learn how to screen cryo-specimens and assess their suitability for high-resolution studies.
  • To learn how to perform high-resolution data collection with a Titan Krios or Talos Arctica.

 

What aspects of cryoEM are covered?

We cover all aspects of cryoEM single particle analysis (cryoEM SPA), high-resolution cryogenic electron tomography (cryoET), or cryogenic electron diffraction (cryoED) including cryo-specimen preparation, grid screening, and high-resolution data collection and preprocessing.  However, as this training program is project and trainee tailored, specific topics are emphasized as needed for the trainee's project and skill/experience level.

Who can apply for project-tailored training?

Trainees from different experience levels and professional backgrounds, such as principal investigators, faculty, staff, postdocs, or graduate and undergraduate students, are eligible to apply.

What are the training application review criteria?

All project applications are reviewed and approved by an external project evaluation committee.  Review criteria are based on the mission of the S2C2 set forth here.  Briefly, access to this resource is based on the feasibility and scientific merit of the project proposed, biospecimen readiness, the cryoEM research experience of the investigators, geographic diversity, and the status of the applicants' access to SPA-cabable cryoEM facilities at either their home institution or elsewhere.

Safety and biohazardous material concerns will be reviewed by the Stanford Health and Safety Department's Biosafety & Biosecurity Group and the SLAC Environment, Safety, and Health Division's Biological Safety Program.

Is project-tailored training remote or in-person?

In short, both.  Training in cryo-specimen preparation, grid screening, and high-resolution data collection and preprocessing can be done remotely over Zoom; however, in-person hands-on traiining is preferred, especially for cryo-specimen preparation.

What length of project-tailored training can be requested?

  • Any suitable period from one week to six weeks of non-contiguous training sessions.
  • The period of training and number of sessions will be determined by the applicant's need, biospecimen readiness, and available space at S2C2.

 

What are the trainee obligations?

All users must be registered in the SLAC User Portal and meet all SLAC/DOE access requirements to use the cryoEM facility which includes safety training, an institutional user agreement, and additional documents to be uploaded.

S2C2 provides technical tools and staff support for world-leading science at no charge with the understanding that significant results are to be publicly disseminated.  Users must therefore acknowledge in publications the NIH grant that supports facility operations, the supporting S2C2 CryoEM Specialist, and the specific microscope(s) used.  Acknowledging the supporting S2C2 CryoEM Specialist is especially appreciated.  Expected acknowledgement wording grant number, and co-authorship policy can be found here.  Please inform us of your published results by emailing S2C2@slac.stanford.edu.

What is the cost of training?

None, for academic & nonprofit trainees.  No fees will be charged for training, microscope time, or study materials.  The expenses associated with running and maintaining the facility and staff compensation are borne by S2C2 federal funding from NIH; however, expenses for trainee transportation, local room and board, and shipping of samples (and dewar return shipping) will be borne by the trainee and their home institution. 

Will any reading material be provided?

Successful training applicants will receive online reading material, including video clips and PDF copies of material, as needed.

Process for Accessing the S2CProject-tailored CryoEM Training Program

Communication with the S2C2 Operations Team
  • The S2C2 User Administrator is your administrative point of contact during steps 1-4 and will timely share evaluation outcomes, coordinate SLAC user onboarding, invite microscope time requests, and confirm your scheduled microscope session(s) with the trainee via email.
  • The S2CCryoEM Specialist running the project-tailored training program is your scientific point of contact during steps 6-10 and will email the trainee about two weeks before your training to aid with logistics and answer any additional questions you may have.

1. Project-tailored CryoEM Training Program Application, Submission, & Evaluation

Participation in the project-tailored SPA training program at S2Ccan be obtained by submitting a project-tailored training project application through the SLAC User Portal.  All project participants, both new trainees, principal investigators, and project collaborators, need to register on the SLAC User Portal before proceeding with a project-tailored training project appllication.

Cyclic Application Deadline: Project-tailored training project applications are due the first day of each month.  With few exceptions, applications will be reviewed within the same month and results communicated by the following deadline.

Application Materials:  Project-tailored training project application materials consist of a title and abstract, a proposed length of training, remote or in-person training request, specific SPA workflow trainings requested, a training and experience document covering goals & motivation, current research, institutional impact, cryogenic electron microscopy experience, other electron microscopy experience, and operational experience, a project description covering aims & impact, feasibility & preliminary data, proposed experiments, goals & expectations, and project expertise & resources, preliminary data figures, publication history, biosafety information, and support documents consisting of a preliminary data figures document, a publication history, a trainee biosketch or curriculum vitae and a PI biosketch or curriculum vitae (optional), project personnel details, and funding sources.  Futher details may be found here.

Project Evaulation: Proposed projects are sent to an external project evaulation committee and review criteria based on the mission of the S2Care are set forth here.

Evaluation Outcome: The outcome of your project-tailored training project evaluation will be timely communicated to applicants by the S2CUser Administrator and those awarded approval will be invited to request microscope time and proceed with onboarding.

2. Institutional User Agreement

The Stanford-SLAC CryoEM Center is located on the premises of a Department of Energy national laboratory.  The DOE requires that a stand-alone CryoEM User Agreement, or addendum to an existing DOE User Agreement that covers experiments at SSRL and LCLS, must be executed before the beginning of any experiment.  Once executed, the agreement will cover cryoEM experiments for any group from that institution.  The list of institutions that have existing User Agreements with SLAC can be found here with instructions on obtaining institutional user agreements if your institution doesn't yet have an existing agreement on file.

3. SLAC User Onboarding

The S2CUser Administrator will coordinate the trainee's SLAC user onboarding.  Onboarding involves requesting a SLAC ID number (prerequisite for other onboarding requirements), requesting SLAC Unix and Window Accounts, and taking an initial online safety and security training.  A user security/safety badge is obtained after completing the in-person safety orientation once you are onsite.

4. Microscope Time Requests

Microscope Time Requests are submitted through the SLAC User Portal after your comprehensive training project is awarded cumulative microscope time.  Sample details and deviations from the originally proposed project are to be included in the request.  The details of the samples to be brought to SLAC must be provided in the microscope time request.  This information is used to determine if biosafety requirements are satisfied.  The S2CUser Administrator will allocate time and schedule your microscope session after microscope time requests have been revceived and biosafety requirements are satisfied.  All microscope sessions start and end at 9:00 am pacific time and are scheduled on a first requested first scheduled basis.

Time Request Materials: Time request materials consist of project information, instrument information, sample information, supporting preliminary data, scheduling requests, and participating project personnel.  Further details may be found here.

5. Lodging and Traveling to SLAC

Rooms are reserved for users of our CryoEM Facility at the Stanford Guest House situated at SLAC.  you will be asked to provide information about the dates of your scheduled session and your assigned proposal/project number.  SLAC's Visitor, User, and Employee (VUE) Center has an Accommodations page with alternative lodging options.  For assistance in arranging transportation to SLAC and local accommodations, trainees should contact our administrative associate, as needed.

6. Sample Shipment to & from SLAC

Sample(s) should be shipped overnight/express to SLAC Monday through Wednesday the week prior to the date of your assigned microscope session to ensure timely arrival before the weekend.  Express packages are delivered to the SLAC Receiving Department at 10:00 am Monday - Friday (excluding holidays), and subsequently delivered to the cryoEM facility.  Frozen samples left in transit ove the weekend usually crystallize or thaw completely rendering them unusable.

Complete the form linked here to generate the required shipping lables to & from SLAC.  The dry cryogenic shipping dewar and sample boxes/buttons (and sample grids, if requested) will be sent back to the users one week after the microscope session.  We can store frozen grids during the project period.  The user is responsible for all shipping costs.  See this shipping page for more detials, including international shipments.

7. Project-tailored Training Schedule

The daily agenda/schedule for your project-tailored training is coordinated with your Scientific Point of Contact (SPOC), i.e., the S2CcryoEM specialist providing your training.  Your SPOC will provide reading materials and training in cryo-specimen preparation, grid screening, and data collection.

8. Microscope Session & Remote Access

Microscope sessions are coordinated with and supported by your Scientific Point of Contact (SPOC), i.e., the S2C2 cryoEM specialist supporting your microscope session.  Typically, remote users are provided observational access over Zoom with their cryoEM specialist, who is operating and physically present at the microscope.  A typical microscope session workflow can be found here.

Secured remote access to operate the cryo-electron microscopes is available for qualified users and can be provided based on their needs through the cryoEM specialist supporting the microscope session.

9. Data Access & Transfer

Experimental data will be made available to the user through SLAC's central data storage computer cluster.  A SLAC Unix account is required to access the data.  Standard Unix tools like SCP and RSYNC are available, as is Globus.  Further details here.

10. Post Project-tailored Training Support

After your project-tailored training concludes, our cryoEM specialists will continue providing remote support via email and Zoom, as needed, for up to one year post training.

11. Data Storage & Preprocessing

SLAC will provide short term storage, i.e., two months, on disk and long-term storage, i.e., two years, on magnetic tape.  On-the-fly preprocessing, alignment, and CTF estimation to evaulate image quality is available via Slack Channel.