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 CryoSample/Data

CryoSample – ASCEM Vitrobot Training and Service Guidelines
  Agreement for the Regulations of Vitrobot
  The cryo-grid preparation by Vitrobot is the most critical step to obtain a high-resolution cryoEM structure. However, every bio-sample has unique properties and is preserved in different buffer solutions, resulting in different optimal conditions for cryo-grid preparation. Moreover, many factors can influence the final outcome of cryo-grid preparation, so it is best that users who know the sample well prepare/test the cryo-grid preparation. In addition, due to the limited manpower, it is indeed difficult for ASCEM to provide customized cryo-grid service for every user. For Vitrobot applicants, ASCEM provides basic training and certification for users from Academia Sinica. A certified user can prepare or test their own cryo-grid (cryo-sample) with various experimental conditions.
 
 
Q1. Why is Vitrobot operation limited to certified users from Academia Sinica?
A1. To ensure facility safety, only users with Academia Sinica Employee ID Card are allowed to enter the site without being accompanied by staff. In addition, to maintain ASCEM Vitrobot and to ensure its service quality to all applicants, only certified users from Academia Sinica are allowed to operate ASCEM Vitrobot without any supervision.
Q2. In what condition can ASCEM assist to operate Vitrobot for users from Academia Sinica?
A2. If the need is occasional and sample is relatively simple (e.g. liposome); or when a project is urgent and the user cannot be certified in time, ASCEM can assist to prepare cryo-grid. The regulations are described in A3.
Q3. Alternatives for non-Academia Sinica Vitrobot applicants
A3. Some other cryoEM institutes in Taiwan, e.g. Institute of Physics of NTU, NCKU, NSRRC, and Genomics Research Center of AS, are also equipped with Vitrobot or equivalent sample preparation instruments for cryoEM structure determination. Non-AS users are recommended to do cryo-grid preparation there.

Alternatively, non-AS user may collaborate with a certified member of an AS lab or with Taiwan Protein Project team (http://tpp.ibc.sinica.edu.tw/en-index.php).

If a direct use of ASCEM Vitrobot is still a necessary, user may apply for staff operation. Please follow the regulations.


 
Regulations for ASCEM assistance on Vitrobot operation (based on the ASCEM’s principle for equipment application and reservation) :
1. User can apply ASCEM assistance on Vitrobot operation as needed. Additional fee will be charged as NT$1,000 per time for campus users and NT$2,000 per time for off campus users.
2. User needs to contact and fully discuss with the facility managers before submitting a “Service Request” for Vitrobot2 on DAAIS Online Facility Reservation System. The available time slots are 14:00-16:00, Monday through Friday.
3. The samples need to be delivered to the staff before the machine time. If the samples are not delivered on time, no make-up will be offered and the fee will still be charged according to the regulations.
4. A maximum of 4 cryo-grid samples will be made by the staff each time. If the 4 cryo-grids are all failed (see images), the staff will re-produce one more time without charging the staff-operation fee for the reproduction, but the user still needs to pay for Vitrobot using and consumables.
5. User needs to communicate with the staff about the sample state and the conditions for making cryo-grid samples, otherwise the common equipment settings will be adopted for the procedures.
6. The conditions for preparing cryo-grid samples are the consensus between the staff and the user, user needs to understand that the ice thickness of the cryo-grid samples will vary depending on the sample state and also, there is no guarantee that the ice thickness will meet the experimental requirements.
7. The pre-treatment of the cryo-grids is not covered by the staff, such as grid cleaning and various coating.
8. Samples with biosafety concerns need to be approved by ASCEM Steering Committee first. Please submit your application via the Google form (including Vitrobot) and the Requirements and Affidavit should be attached.
Failed cryo-grid production Not failed cryo-grid production
 
Data – On-the-Fly Motion Correction Service (2022.02)
 
To speed up the implementation of various important experiments, ASCEM is equipped with on-the-fly motion correction service for CEM3/4 users with common parameters based on the past experience of facility.
1. Service application: Please choose the requirements while submitting a “Service Request” on DAAIS Online Facility Reservation System.
 
 
For using preset parameters, please choose “Yes (Default Parameter)”.
For modifying parameters, please reach a consensus with your PI first, then choose “Yes (User defined parameter)” and remark new parameter values.
2. Data transfer and storage
 
On-the-fly motion correction Service Output files Default Mode for Data transfer
Use corrected images Data is transferred to ASGC by ASCEM.
raw images User brings own storage device to ASCEM for data download and saving.
(Please contact Facility Managers for exceptions.)
Not Use raw images User brings own storage device to ASCEM for data download and saving.
(Please contact Facility Managers for exceptions.)
 
User data will be periodically deleted to release facility computer resource for continuous data input. Basically, CEM3 will keep experiment data for two months, and CEM4 three months. Any change will be notified by Facility managers.
The data computing and storage services provided by ASGC will follow the regulations of ASGC, including charging schemes.
 
Data – ASGC Account & DiCOSAPP data handling (2019.08)
 
Account application
  For Academia Sinica user, you may directly use SSO to sign up.
For Non-AS user or those who don’t have SSO, please apply a DiCOS Account.
DiCOSAPP Data Handling
  Overview
  If you confront any problem about ASGC account, please contact via EMAIL cryoem@gate.sinica.edu.tw.
  For technical problems, you may contact Mr. Tsung-Hsun Wu DiCOS-Support@twgrid.org
Pay-for-Use CryoEM Data Storage and Computing Resource
  To ease the need for large data storage of cryoEM studies, ASCEM-ASGC provide a pay‐for‐use CryoEM Group Space service for data storage. An independent directory will be created for each user group and the group PI will be the contact person for the service management.
  The charge for the Space is NTD 1,000 for 1TB per year. The fee covers from Jan 1st to Dec 31st in a year. Users can always add more storage space anytime, but it still ends at Dec 31 of the same year. The charge will be paid as the way for facilities usage. Users within Academia Sinica (AS) will pay for the usage via intramural budget accounts and users outside AS will receive a payment notice for further instructions.
  Users should acknowledge TPP, ASCEM and ASGC in the publication if computing resource is used.
  For the policies of accounts and data storage/deletion management, please read the instructions (ASCEM-ASGC Resource Usage for CryoEM Data Storage and Computing).
 
 

Contact: Academia Sinica CryoEM Facility   Email:cryoem@gate.sinica.edu.tw

No. 128, Sect. 2, Academia Rd., Nankang, Taipei 115, Taiwan (R.O.C.)      TEL:+886-2-27872572

(Lab) B2-I04 (Interdisciplinary Sci. & Tech. Building), No. 28, Ln. 70, Sec. 2, Academia Rd., Nankang, Taipei 115, Taiwan (R.O.C.)

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