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