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

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

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

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

How does it work? Information Handling PlasmID:

Organization of Data in PlasmID CLONE VECTORINSERT GENE

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

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

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

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

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

Status of Depositors Agreements SiteInstitutionPSI-XStatus CESGUniversity of WisconsinPSI-2completed JCSGGNFPSI-2completed MCSGWUSTLPSI-2completed NYSGRCSGXPSI-2completed BSCGLBLPSI-1in process SESGCUGAPSI-1completed UAHPSI-1in process ATCG3DDeCODEPSI-2completed MCSGUniversity of TorontoPSI-2completed JCSGTSRI/ScrippsPSI-2in process MCSGANLPSI-2in process NYCMPSColumbiaPSI-2in process NYSGCRutgersPSI-2in process CHTSBUniversity of RochesterPSI-2completed UABPSI-1in process CSMPUCSFPSI-2in process NYSBCPSI-2completed ICSFILANLPSI-2in process

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

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

Updates to Clone Submission Forms Excellent suggestions and input from many researchers at several PSI sites Five key documents 1.Submission Checklist 2.SitenameVectors 3.clone_files_PSI_table details 4.Definitions_for_annotating_CDS_sequences 5.Submission Timeline

Formatting Column HeaderRequired?DescriptionExample UniqueCloneIDYPSI site internal ID _GO.880 (from CESG) VectorYVector Name (from table provided) PDBIDNProvide a PDB if this clone resulted in a structure 1I6C NTSeqYtext string of the inserted sequence acggcgcgagtgttgtg … CDSstartYstart of CDS relative to insert NT Seq 1 CDSstopYStop of CDS relative to NT Seq 300

YFG His Ex. BamHI or AttL1Ex. SalI or AttL2 CDS startCDS stop YFG Flag Ex. BamHI or AttL1Ex. SalI or AttL2 CDS startCDS stop GFP YFG Ex. BamHI or AttL1Ex. SalI or AttL2 CDS startCDS stop YFG Ex. BamHI or AttL1Ex. SalI or AttL2 CDS startCDS stop GFP YFG Ex. BamHI or AttL1Ex. SalI or AttL2 CDS startCDS stop His CDS Definitions “Fusion” Format “Closed” Format

PSI-MR Timeline PSI Site Data Submission Sample Submission 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 site reviews documents and s PSI-MR with any questions ≤ 1 week PSI site compiles data and sends to PSI-MR for review 2-4 weeks PSI-MR and PSI site work together to create computer compatible formatted files PSI site prepares samples and sends to PSI-MR ≤ 1 week2-8 weeks PSI-MR works with PSI site to acquire suitable samples 1 week 1-2 weeks 2 days

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

Data and sample import # imported# sequenced# available >2000 CESG NYSGRC JCSG ATCG3D ~ Bottlenecks Format of data Send data BEFORE samples Timeline

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

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

PlasmID demo

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

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

PSI-MR portal demo

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

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