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PSI Materials Repository:
Goals and Progress
Josh LaBaerDirector, 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: http://plasmid.hms.harvard.edu
Organization of Data in PlasmID
CLONE
VECTOR INSERT
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 contactCollect & curate info on vectorsEstablish 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 AgreementsSite Institution PSI-X Status
CESG University of Wisconsin PSI-2 completed
JCSG GNF PSI-2 completed
MCSG WUSTL PSI-2 completed
NYSGRC SGX PSI-2 completed
BSCG LBL PSI-1 in process
SESGC UGA PSI-1 completed
UAH PSI-1 in process
ATCG3D DeCODE PSI-2 completed
MCSG University of Toronto PSI-2 completed
JCSG TSRI/Scripps PSI-2 in process
MCSG ANL PSI-2 in process
NYCMPS Columbia PSI-2 in process
NYSGC Rutgers PSI-2 in process
CHTSB University of Rochester PSI-2 completed
UAB PSI-1 in process
CSMP UCSF PSI-2 in process
NYSBC PSI-2 completed
ICSFI LANL PSI-2 in process
Current Goals
Create points of contactCollect & curate info on vectorsEstablish 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 documents1. Submission Checklist2. SitenameVectors3. clone_files_PSI_table details4. Definitions_for_annotating_CDS_seque
nces5. Submission Timeline
FormattingColumn Header Required? Description Example
UniqueCloneID
Y PSI site internal ID 917.1.71_GO.880 (from CESG)
Vector Y Vector Name (from table provided)
PDBID N Provide a PDB if this clone resulted in a structure
1I6C
NTSeq Y text string of the inserted sequence
acggcgcgagtgttgtg…
CDSstart Y start of CDS relative to insert NT Seq
1
CDSstop Y Stop of CDS relative to NT Seq
300
YFG His
Ex. BamHI or AttL1 Ex. SalI or AttL2
CDS start CDS stop
YFG Flag
Ex. BamHI or AttL1 Ex. SalI or AttL2
CDS start CDS stop
GFP
YFG
Ex. BamHI or AttL1 Ex. SalI or AttL2
CDS start CDS stop
YFG
Ex. BamHI or AttL1 Ex. SalI or AttL2
CDS start CDS stop
GFP
YFG
Ex. BamHI or AttL1 Ex. SalI or AttL2
CDS start CDS stop
His
CDS Definitions
“Fusion” Format
“Closed” Format
PS
I-M
RT
imel
ine
PS
I S
ite
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 emails 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 week 2-8 weeks
PSI-MR works with PSI site to acquire suitable samples
1 week
1-2 weeks
2 days
Current Goals
Create points of contactCollect & curate info on vectorsEstablish 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
JCSGATCG3D
~1400 761
Bottlenecks•Format of data•Send data BEFORE samples•Timeline
Current Goals
Create points of contactCollect & curate info on vectorsEstablish 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
http://plasmid.med.harvard.edu/PLASMID/
Current Goals
Create points of contactCollect & curate info on vectorsEstablish 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
http://www.hip.harvard.edu/PSIMR/index.htm
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/NIGMSJean Chin
PSI KBHelen Berman
Andrei KouranovWendy TaoRaship Shah
John Westbrook
All PSI Sites
Funding:
Cathy CormierJanice Williamson
Helen TaycherYanhui Hu
Dongmei ZuoAndreas Rolfs
Tina KelleyMike Collins
Jason KramerApril Pierce
Li ChanDan Schiwek
Jason Xu
Stephanie Mohr