PNCC resources are open to everyone in the global scientific community who wants to learn CryoEM. Access is given out based on peer reviewed proposals.
No cost for services and training.
This depends on your scientific objectives. Limited access receives 8-24hrs of instrument time, focused for preliminary data. General access receives up to 20 days per year with up to 2 years of access, allocated in 5 day increments. This is for long-term significant impact research and cross-training opportunities. More information can be found on Proposal Templates themselves.
All proposals are sent for review monthly and are due by 11:59pm on the 1st of that month.
Should I include preliminary data?
Yes, this helps reviewers establish feasibility of the project. If your proposal is missing preliminary data, if approved, it might receive reduced allocated hours. If you don't have preliminary data, apply with our Limited access proposal. We provide screening services at PNCC to get preliminary data.
There is no limit to the number of General Access proposals a PI may have as long as the science focus is distinct and non-overlapping. A PI may only have 1 active Limited Access proposal at any time.
PNCC can only work with samples that are categorized biohazard safety level (BSL) 1 and 2. If the sample is, or is derived from, or contains any agent (or its DNA) that can be infectious or toxic in humans, animals or plants (viruses, bacteria, toxins etc.), or is obtained from sources that could potentially harbor (latently) such agents (eg. serum-derived or obtained from human cell lines), then the risk group (RG) must be established, licenses for shipping obtained, and safe operating procedures defined according to biohazard safety level. Additional guidance on risk groups can be found in Section II of the CDC BMBL 5th Edition and references therein. The starting point for our review will be the approval from the Institutional Biosafety Committee (IBC) from the applicant's home institution and the protocols on which the approval is based, so please attach both to this proposal after the biosketches. If your final sample might be considered RG1 but preparative work involved steps at BSL2, then a copy of your home-institution IBC approval indicating a down-grading of BSL during the purification will be needed to support that designation. Generally, center staff will oversee approval of RG1 agents, while acceptance of RG2 agents from US institutions will require involvement of OHSU's biosafety officer / IBC which may impact project award timeframes. Shipping of agents from outside the US often requires additional approval from the CDC and/or USDA, and will be considered on an individual basis. We cannot receive BSL2 samples in liquid form at this time. Only pre-frozen BSL2 samples with IBC documentation can be handled.
Please email our User Coordinator any questions regarding editing proposals, including adding users.
It takes approximately 45 days for proposal to be approved at this time. If it has been longer than this, please email our User Coordinator.
In the EMSL User Portal, select proposal, on new page select “Peer Reviews.”
Limited Access expires 3 months after approval. General Access can have access for up to 2 years, but each 120 hours allocation expires in 6 months if not used.
If you applied with a Limited Use (or our previous proposal types: Standard or Rapid), then you will need to apply with a new proposal. If you have a General Access (or our previous proposal type: Programmatic), then you will need to submit an Allocation Renewal. With a General Access proposal, you can pre-apply for more time after you have used 60% of your allocated hours (72 hours) by submitting an Allocation Renewal early.
You can only add more samples to a General Access Proposal during an Allocation Renewal. During this time, you can add up to 5 samples, which are restricted to samples that align directly to the original proposal and builds upon the prior samples. All samples will be checked by our Co-Director Claudia Lopez. Any samples that are found to be outside the scope of the proposal will not be approved to be shipped on-site.
You must have a PNCC Use and Access Agreement on-file (and Unescorted Visitor Information Form for on-site visits). See the User Onboarding webpage for more details. Once your paperwork is completed, contact your Scientific Point of Contact (SPOC) to schedule the session.
There is a limit of 2 users visiting on-site. Special arrangements can be made, contact your PNCC SPOC.
Yes, but please be aware of our cancellation policy in our scheduling policies.
Each awarded proposals can only book 5 days at a time and a minimum of 4 hours.
Samples must be pre-screened before requests for Krios time are accepted. This means that we must either receive images of samples analyzed under cryo-conditions or be given a strong argument for biochemical mastery of the sample. If your samples are found to be of low quality, then your reservation time will be forfeit.
Ship your grids any day after Monday, but please make sure that we can receive them by Friday. Please include in the dry shipper a FedEx label to return the dewar and a copy of your grid submission form. Once you have the FedEx tracking number for this shipment please forward this by email so we can track it. As soon as we receive the shipment we will let you know. Please send the dry shipper to:
Att: Claudia López
Oregon Health & Science University
LVMS Mail Code: CL-P
2730 SW Moody Ave
Portland OR 97201
Per our scheduling policies, we request that only 11 grids are shipped to be screened in an 8 hour screening session. Up to 4 grids can be loaded for a scheduled data collection reservation.
All proposals have up to 4hrs of SPOC time for sample preparation (should be used in the same day). After the allocated 4hrs, users should send frozen grids or come on-site to receive training on preparing their own samples. Please be aware that if your SPOC needs to clip grids, your session might be delayed. If your group does not have access to a clipping station at your institution, we can provide you a information needed to purchase one from ThemoScientific. Please contact our Co-Director Claudia Lopez for more information.
Yes, only if the samples have been included in the proposal's sample table AND are BSL-1. We currently cannot accept liquid BSL-2 samples. Users will have access to a Vitrobot and Leica GP2 for sample preparation. All proposals have up to 4hrs of SPOC time for sample preparation or training on these equipment.
This depends. All requested samples MUST be in the same scientific scope to be approved. During the General Access Allocation Renewal, approved users can request additional samples be added to their proposal. If BSL-2 samples are added, we will require a copy of your Institutional IBC for approval. Please contact our Co-Director Claudia Lopez in all other cases.
We offer 3 routes for you to access your PNCC data.
- The fastest transfer option is using GLOBUS and this is the preferred method since you can get near real-time access to the data as it streams off the microscope and detector. GLOBUS also provides a single point of access for you to see old and new data using a single endpoint rather than needing separate download links for each dataset. However, not all institutions permit GLOBUS transfers inbound. PNCC now requires each proposal to list the GLOBUSID for at least 1 team member at time of proposal submission. Once your project is approved the PNCC Data Transfer Team will reach out to the PI and team to do a test transfer via a shared endpoint to confirm if GLOBUS works for you and to establish expected transfer speeds to your local storage. Setting up GLOBUS access is pretty straightforward and is completely free for academics and non-profits. To get the ID go to https://www.globusid.org/create where you can register for a GLOBUS basic account if your institution doesn’t already have an institutional license.
- The second fastest transfer option to download PNCC data is to use the ARIA2 parallel download manager. For every dataset collected an autogenerated email will be sent to members of the team to notify that data is available for download. However, this option is only available after a microscope session is complete and the full dataset has been uploaded to the archive. Installation of ARIA2 is straightforward with options to compile from source or direct download of binaries for OS X and Windows. Once installed, the use of ARIA2 is very easy. At the bottom of each PNCC autogenerated dataset email is a link for specific use with ARIA2 which points to the particular dataset. Simply copy this link and launch it with the ARIA2 command line to initiate the transfer. Similar to GLOBUS, if your local connection is intermittent or the download gets halted, ARIA2 will automatically resume after disruption. ARIA2 parallelized download options are particularly helpful for big files or when data transfer rates are slow between your institution and the PNCC archive.
- The slowest but most accessible transfer option is via the EMSL User Portal “Get Data” tab. To access the datasets, login to the EMSL User Portal then either migrate to the “Get Data” tab OR click the MyEMSL data download link provided in the autogenerated email mentioned above. Note: The portal login gives you a token needed to see the data and the token times out after awhile. So if you have problems seeing the data try logging in to the portal on another browser page then refreshing the data portal page.
Please contact your PNCC SPOC for this. We are hoping to add this to our downloaded data.
Yes, this must be approved by your PNCC SPOC before shipping hard drives to our facility.
Acknowledgements required for all research publications and presentations supported by use of PNCC:
- For all presentations and posters, a shortened acknowledgement is acceptable. Include the exact phrase “Use of Pacific Northwest Center for Cryo-EM supported by NIH grant U24GM129547” on any Acknowledgements/Funding paragraph or slide.
- For all research publications or press releases, the full acknowledgement is required. Include the exact phrase "A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at OHSU and accessed through EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research" in the appropriate Acknowledgements/Funding section.
- If PNCC staff only provided standard specimen and data services then co-authorship is not warranted. Instead, please recognize the expert assistance of center staff (credited by name) in the acknowledgements section of the publication.
- If on behalf of a user, PNCC staff developed new methods that were required to attain the data used in a publication, then PNCC staff co-authorship is warranted.
- In cases where PNCC staff make significant intellectual contributions to a published study in the course of providing research guidance and/or cross-training, then co-authorship is expected.
- All imaging and other data generated by PNCC must be made public following established accepted practices for data validation and deposition to publicly accessible worldwide repositories (EMDB or PDB) prior to manuscript publication. Additionally, all raw and initial processed datasets acquired by PNCC will be archived using the MyEMSL archive. Users can access their project related archived data anytime and anywhere via the “Get Data” tab within the EMSL User Portal. Data is owned by the user during the awarded proposal period and for 1-year following the end of the respective user proposal. During this window only the proposal PI, their designated team and PNCC staff can access the data. However, 1-year after the end of each individual user proposal, all associated data for that specific proposal is made publicly searchable within MyEMSL and is available to the general scientific community. The archiving of PNCC data is automatic and does not remove the requirement to deposit data related to individual publications in worldwide repositories.
Public access to publications for dissemination of information and tracking purposes by NIH and PNCC:
- NIH requires that all research papers describing research supported by the use of PNCC must be available to the public through PubMed Central. Additionally, NIH requires that PNCC have a copy of all resulting publications and information on all deposited structures/maps. All users of PNCC are therefore required to report all journal articles, conference proceedings, books or book chapters, contributed news articles, et cetera that include data generated by use of PNCC. Authors must upload these documents to the EMSL User Portal and link it to their awarded project within 2-weeks of publication.