PSI Materials Repository: Goals and Progress

1. PSI Materials Repository:Goals and Progress Josh LaBaer Director, Harvard Institute of Proteomics Harvard Medical School

2. Who are we?Harvard Institute of Proteomics • High-throughput methods for biomarker, antigen and interaction discovery; cell-based screens; other functional assays • Clone production—ORF cloning for human genes and several microorganisms • Plasmid repository established 2004 • Currently >80,000 clones • Plasmid information curated by a PhD level scientist prior to import • Plasmid Information Database (PlasmID) • Requests daily, distribute world-wide

3. Arrive as DNA Liquid Culture Transformation & Robotic Colony Pick How does it work?Receiving Plasmids Working sample 1 or more on-site archival sample • Phage-resistant cells • Sequence Verified • Barcode labels • Automation

4. How does it work?Storing Plasmids • BioBank Features • Two -80 freezers • Total sample capacity of 160,000 • Samples stored in 2D barcode-labeled tubes • BioBank Software integrated with PlasmID (Thermo, Zmation)

5. How does it work?Information Handling PlasmID: http://plasmid.hms.harvard.edu

6. Organization of Data in PlasmID

7. On-Line Request Automated Retrieval Timely Delivery How does it work?Delivery

8. Overall Goals of the PSI-MR • Centralized storage & distribution of information and samples for the >100,000 plasmids created at PSI sites • Quality analysis and control at every step • Barcode labels and Information Tracking at All Steps • Single Colony Selection & Use of Phage-Resistant Bacterial Host Strains • End read Sequencing & Analysis • State-of-the-Art Freezer Storage System (BioBank) • Scientifically Curated plasmid Information in Oracle Database (PlasmID) • Saves searchable information about all plasmids • Linked to PSI Knowledgebase • Ordering directly from website • Develop terms under which plasmids can be distributed under minimally restrictive terms • Depositors Agreement and Expedited Process MTA

9. Early Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Establish clone submission format • Transfer of information to PSI-MR • Update PlasmID to reflect connection to PSI • Transfer of samples to PSI-MR • Create PSI-MR website

10. Current Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Establish clone submission format • Transfer of information to PSI-MR • Transfer of samples to PSI-MR • Update PlasmID to reflect connection to PSI • Create PSI-MR website

11. Depositors Agreement • Agreement that sets the terms for distributing plasmids deposited by the PSI-MR sites • Why do we need a DA? • Gives the Materials Repository permission to distribute the property of others • Expressly prohibited by MTAs • Appropriately assigns responsibility for the safety of distribution • MTAs do not address these issues • Universal set of operating conditions • Establishes the MTA that will accompany the clones

12. Status of Depositors Agreements

13. Current Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Continue to work with PSI institutions and PIs to get the Depositors Agreement Signed • Establish clone submission format • Transfer of information to PSI-MR • Transfer of samples to PSI-MR • Update PlasmID to reflect connection to PSI • Create PSI-MR website

14. Data Processing, Data Validation Import Files (tab-delimited) Maps (PDF) Sequence (txt) Custom Database or Tab-Delimited files (formatted files) Import into PlasmID, Data Validation “Dictionary” of Controlled Vocabulary Other Formats (e.g. Plasmid Maps) Import Files (tab-delimited) Maps (PDF) Sequence (txt) Scientific Curation, Data Validation Information Processing

15. Updates to Clone Submission Forms • Excellent suggestions and input from many researchers at several PSI sites • Five key documents • Submission Checklist • SitenameVectors • clone_files_PSI_table details • Definitions_for_annotating_CDS_sequences • Submission Timeline

16. Formatting

17. Ex. BamHI or AttL1 Ex. SalI or AttL2 YFG His CDS start CDS stop Ex. BamHI or AttL1 Ex. SalI or AttL2 YFG Flag GFP CDS start CDS stop Ex. BamHI or AttL1 Ex. SalI or AttL2 YFG CDS start CDS stop Ex. BamHI or AttL1 Ex. SalI or AttL2 YFG GFP CDS start CDS stop Ex. BamHI or AttL1 Ex. SalI or AttL2 YFG His CDS start CDS stop CDS Definitions “Fusion” Format “Closed” Format

18. Send PSI site submission checklist and templates PSI-MR reviews data and communicates with PSI site about any changes PSI-MR contacts PSI site to send their samples PSI-MR receives samples, inputs data, and sequences samples. PSI-MR re-arrays samples, inputs data into PlasmID and makes clones available for purchase PSI-MR PSI-MR and PSI site work together to create computer compatible formatted files PSI-MR works with PSI site to acquire suitable samples PSI site compiles data and sends to PSI-MR for review PSI site reviews documents and emails PSI-MR with any questions PSI site prepares samples and sends to PSI-MR PSI Site ≤ 1 week 2-4 weeks ≤ 1 week 2-8 weeks 1 week Timeline 2 days 1-2 weeks Data Submission Sample Submission

19. Current Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Continue to work with PSI institutions and PIs to get the Depositors Agreement Signed • Establish clone submission format • Send these documents to PSI sites • Transfer of information to PSI-MR • Transfer of samples to PSI-MR • Update PlasmID to reflect connection to PSI • Create PSI-MR website

20. Data and sample import • Bottlenecks • Format of data • Send data BEFORE samples • Timeline

21. Current Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Continue to work with PSI institutions and PIs to get the Depositors Agreement Signed • Establish clone info deposit format • Send these documents to PSI sites • Transfer of information to PSI-MR • Transfer of samples to PSI-MR • Update PlasmID to reflect connection to PSI • Create PSI-MR website

22. What’s new on PlasmID • PSI specific searches • TargetDB/PepcDB ID • Protein expression, solubility, or purification • PDB ID • PSI site • Plasmids linked to PSI Structural Genomics Knowledgebase by TargetDB ID • Credit cards now accepted for all plasmid purchases • PayPal account NOT required

23. PlasmID demo http://plasmid.med.harvard.edu/PLASMID/

24. Current Goals • Create points of contact • Collect & curate info on vectors • Establish Depositor Agreements • Continue to work with PSI institutions and PIs to get the Depositors Agreement Signed • Establish clone info deposit format • Send these documents to PSI sites • Transfer of information to PSI-MR • Update PlasmID to reflect connection to PSI • Transfer of samples to PSI-MR • Create PSI-MR website

25. PSI-MR Web Portal • Has most up to date clone submission templates • Contains information on how to search for and purchase plasmids on PlasmID • Links to PSI-KB and all PSI Modules and Sites • FAQs about PSI-MR, Depositors Agreements and MTAs

26. PSI-MR portal demo http://www.hip.harvard.edu/PSIMR/index.htm

27. Future Goals • Have all depositors agreements signed • Expedited Process MTA • Continue to process data and samples from PSI sites • Work with other PSI sites to start the submission process • Vector information updates from all PSI sites • Creating an online vector submission module

28. Acknowledgements NIH/NIGMS Jean Chin PSI KB Helen Berman Andrei Kouranov Wendy Tao Raship Shah John Westbrook All PSI Sites Funding: Cathy Cormier Janice Williamson Helen Taycher Yanhui Hu Dongmei Zuo Andreas Rolfs Tina Kelley Mike Collins Jason Kramer April Pierce Li Chan Dan Schiwek Jason Xu Stephanie Mohr