New Research Partnership with Amgen Brings Cryo-EM to USC

Posted on November 10, 2021 by Andrea Renney

0.0.0.1 Phase 1 of the cryogenic electron microscopy (cryo-EM) project is now complete.

Phase 1 of a major collaboration between Amgen, Dornsife, and ITS to establish access to two cryogenic electron microscopy (cryo-EM) instruments on the USC campus is now complete. The microscopes are installed and ready to use with a comprehensive data management and computational processing platform — developed by ITS and CARC — implemented and running.

Cryo-EM is a technique that allows for the study of biomolecular structures at near-atomic resolution for proteins and other biomolecules, without the need for crystallization as required in X-ray crystallography or nuclear magnetic resonance spectroscopy.

The new cryo-EM facility houses two microscopes: Glacios Falcon 4 (manufactured and supported by Thermo Fisher) and Krios K3 (manufactured by Gatan but supported by Thermo Fisher and Gatan). Use of the microscopes will be shared by both USC and Amgen researchers, with data being transferred to either USC storage or Amgen storage accordingly.

CARC’s role in Phase 1 of the cryo-EM project was to develop a comprehensive computational environment for cryo-EM data processing. Major achievements of Phase 1 for CARC were:

  • Automation of data extraction and transfer to CARC storage
  • Automation of data delivery to Amgen’s cloud storage
  • GPU cluster system deployment
  • Development of cryo-EM data pre-processing platform using Pegasus Workflow Management System
  • Development of cryo-EM user portal with integrated Slack user notification feature

The high degree of automation during the data processing, extraction, and transfer process is a huge benefit for researchers making use of the microscopes, and not typically available in cryo-EM workflows. In particular, the integration of Slack as a means to view pre-processed images from the microscopes in near real time will be valuable for monitoring purposes.

This research support-based partnership with a USC school is the first of its kind for ITS. Traditionally, ITS has supported USC schools only through typical IT infrastructure setup and support. Now, this collaboration marks a major milestone in ITS’s (and CARC’s) goal of becoming a long-term collaborative partner for the USC research community.

If you’re interested in using the new microscopes, please contact the Core Center for Excellence in Nano Imaging (CNI) for more information. You can learn about the workflow for using the microscopes in our Using USC’s Cryo-EM Instruments user guide.