WHO WE ARE
The plasmid repository was established in 2004 at the Harvard Institute of Proteomics (HIP) at Harvard Medical School. Our repository holds collections of sequenced-verified open reading frame (ORF) clones made by HIP researchers, and various clones from other researchers throughout the region.
We accept deposits of both large and small clone collections from researchers and distribute their clones to universities across the world. See our slide show for an overview of the repository and how to deposit plasmids.
Q. Do I have to register?
A. You do not have to register to search the database, download vector and clone maps, or view other information. However, you do have to register and sign in before placing an order. Registration is live so you will be able to sign in as soon as you have completed on-line registration. We recommend signing in before you start searching for plasmids because not all plasmids are visible before registration and it saves a few steps later if you plan on ordering plasmids.
Q. My PI is not on the registration list. How do I register?
A. You will need to fill out information for both yourself and the PI during registration. People from the same lab will be able to find their PI on the list the next time someone registers.
Q. I am the PI in addition to being the ?user? who will place orders. How do I register?
A. Please enter your information in both the user and PI fields during registration.
PlasmID Search & Order
Q. How do I search for plasmids?
There are many ways to search for plasmids on PlasmID. You can search by specific terms, such as vector, insert name, CloneID, depositor, TargetDB ID, PDB ID, protein expression, solubility or purification. Click here for all our search options.
Q. I did not find a plasmid of interest in your collection. Am I searching correctly?
A. The most flexible search tool at PlasmID is the Advanced Text Search tool. There, you can use gene names and synonyms, author names, the part or full name of a vector, species name, PDB ID, TargetDB/PepcDB ID or combinations to search plasmids. It is also helpful to use ?official? gene names and identifiers as they appear in databases such as NCBI Entrez Gene or organism-specific databases like SGD or FlyBase. Try ?view empty vectors? to see a list of vectors that take inserts, act as helper vectors, etc. You can enter more than one ID in a field at ?search by gene? to search multiple genes at one time.
Q. How do I place a request for plasmids I identified on PlasmID?
A. Once you identify a plasmid of interest (in a search results table or on a static list, for example), click the button at the far right-hand side of the page to add it to your shopping cart. When you are ready to check out, click the shopping cart icon (top right of any page) to initiate check-out and follow the steps, being sure to click the button at the bottom until your request is confirmed. Click here for more details about how to order.
Q. How do I know if my request went through or when I will receive the plasmid?
A. After you place a request, our system will send a confirmation email. You can sign in at any time to view the status of your request. In addition, you will receive an email when the plasmid is shipped, including FedEx tracking information. Requests are filled in the order in which they are received. Changes day-to-day in the volume and size of requests makes it difficult to tell you the exact day the plasmid(s) will ship, so please check in with the PlasmID system for updates.
Q. Can I view info about the clones I requested and check request status?
A. You can always return to past requests and check request status by signing in and going to "my accounts" (top right of the page). Click on a specific clone order then look for the link at the bottom (# of clones) that takes you to a table of information lets you download an Excel spreadsheet with basic information about the clones.
Q. How much do plasmids cost?
A. Please see current pricing on this page.
Q. How much does shipping cost?
A. There are three ways to pay for shipping:
- Provide us with you FedEx number.
- Flat shipping rate of $10 for domestic orders and $20 for international orders.
- No charge for shipping for the Harvard Medical School community. Pick up your order in the Seeley G. Mudd Building in the HMS Quad in the second floor hallway freezer. You MUST have access to the building to take advantage of this offer.
Q. Why am I charged for a plasmid?
A. These nominal costs are designed to offset the handling fees associated with preparing and sending plasmids. In keeping with the terms outlined by our granting agencies, our aim is always to offset costs, never to make a profit. In addition, we make an effort to significantly reduce the per-clone costs for large collections in order to encourage high-throughput studies.
Q. How can I pay for these plasmids?
A. You can pay using either a credit card or a purchase order number.
Q. Do I need a PayPal account to pay by credit card?
A. No you DO NOT need a PayPal account to pay by credit card. PayPal is only used to securely collect the credit card information. At check out, use the option to ?pay without an account.?
Q. In what form will I receive the plasmids?
A. We usually ship plasmids at room temperature (no ice) as freshly-prepared bacterial glycerol stocks. Our years of experience have shown that plasmids are stable in that format during shipment (streak out and/or freeze at -80 upon arrival). We occasionally ship plasmids as purified DNA in water.
Q. Can I pick up my plasmids from your facility?
A. Yes. During the check out process you may select ?Pick-Up? from the shipping options. Pick up orders will be placed in the hallway freezer in the second floor hallway of the Seely Mudd building. You must have access to this building to request pick up for your shipping option.
Q. How long will it take for me to receive my plasmids?
A. We ask that you please allow 7-10 days from the time that all MTA?s are processed to receive your clone, but many small orders ship much faster. At a minimum filling your order will take three days, however, we fill orders based on the order in which they were received. Also if you place a large order it takes more time to pick the clones, and this can take up to 4 weeks. PLEASE NOTE: We do not ship over the weekend to ensure that people are in your laboratory to receive the order.
Q. Will I need to get a signature on an MTA?
A. For certain plasmids, yes you will need an MTA signature. We will be sure to identify the correct MTA and send it to you electronically to be signed by the appropriate official in your technology transfer office. An original signed copy of the MTA should be returned to the DF/HCC DNA Resource CORE at Harvard Medical School, 240 Longwood Ave, LHRRB, Boston, MA 02115.
More specifically, if you are:
ACADEMIC RESEARCHERS: FLEXGene clones from HIP are covered by a minimally restrictive MTA sent with clones. Most other clones are covered by our standard MTA, which has been pre-approved by some institutions and is based on the well-recognized Uniform Biologicals MTA (UB-MTA). For some clones and for some institutions, however, you will have to get a signed MTA to us before we can send the clones. In a few exceptional cases, you will have to get a third-party MTA signed before we can send the clone, as all or part of the clone is covered by MTAs from more than one institution. For more information about MTAs, including information about how to join our 'in network' group with pre-approved MTA coverage, please contact email@example.com. If you request clones and an MTA is required, the MTA will be emailed to you as a PDF file.
COMPANIES: Most of the HIP FLEXGene clones are available to companies and will be covered by a minimally restrictive MTA between HIP and your company. We will email the MTA after you place a request. You are also welcome to get in touch to review the terms before placing your request.
Q. Can we make this MTA process easier?
A. YES!!! We have developed an Expedited Process MTA that your institution signs and allows all researchers at that institution to receive all plasmids from our collection with only an electronic signature. Please email us if you are interested in starting this process with your institution. Click here for more information about MTAs
HOW TO DEPOSIT PLASMIDS
Q. How do I deposit my clones?
Click here or contact us at firstname.lastname@example.org for more information about depositing clones in our collection. See our slide show for an overview of the repository and the submission process. The three steps to deposit clones are
1. Have your institution sign the Depositors Agreement. This agreement sets the terms by which the plasmid repository will distribute your plasmids. Contact us to see if your institution has already signed a depositor agreement. Otherwise we will contact your technology transfer office to begin the process. Click here for more information about depositor agreements.
2. Prepare the data describing the details about your clones. Because we parse the data directly into our database, we ask that the information you send us is in a particular format. We have submission forms and templates that should guide you in this process.
3. Once we have entered your data into our database, we can accept your plasmid samples. These can be sent on dry ice either as DNA (10-15ul of at least 15ng/ul) or glycerol stocks. If you send glycerol stocks the bacteria MUST BE T1/T5 phage resistant. Once we receive your samples, we will make them available for purchase through PlasmID
Q. What is a Depositors Agreement?
Click here to learn more about the Depositors Agreement.
Q. What is an Expedited Process MTA?
Click here to learn more about the Expedited Process MTA.
Q. What types of plasmids cannot be shared with the repository?
A. Four types of plasmids cannot be added to the repository.
1. Plasmids that require an unusual or specific bacterial host strain cannot be added, as we require that all plasmids are stored here in a phage-resistant DH5-alpha-like host strain, in order to maintain the integrity of the collection as a whole.
2. Plasmids that are identical to material that is commercially available cannot be added to our collection.
3. Plasmids that are hazardous or legally restricted for distribution cannot be added to the repository.
4. Plasmids that you do not have the right to distribute (for example, plasmids you received from another researcher and/or made by another person and/or protected by a patent, licensing agreement, etc.) cannot be shared with us unless permission is also granted by any and all relevant third parties. Sometimes this extends even to modified forms of a plasmid. In general, you can share plasmids that you made or made significant modifications, but you cannot share unmodified forms of something you got from another researcher or a company.
Q. How are plasmids stored and handled after I share them?
A. When you share plasmids with the repository, we transform them into a phage-resistant bacterial host strain, single colony isolate, and create working and archival glycerol stocks. These are stored in conventional -80 degree freezers (archival copies) or in the fully automated BioBank freezer storage system, in which working samples are stored in individually 2D barcode-labeled tubes for automated retrieval and array in any format. Information about each clone is carefully curated by PhD-level scientists and entered into the database.
INFORMATION ABOUT OUR PLASMIDS
Q. What's "closed" vs. "fusion" format?
A. This terminology, adopted from the Harvard Institute of Proteomics (HIP), indicates that a stop codon is present (closed) or is absent (fusion) in a cDNA or ORF insert. For more details about these definitions click here. Fusion format clones are useful for producing C-terminally tagged versions of an ORF.
Q. Can I use restriction enzymes with human clones in pDNR-Dual?
A. The human pDNR-Dual master clones from HIP were generated using the InFusion reaction (Clontech) rather than an RE approach and most of the RE sites in the MCS are gone after the insert is introduced. In the resulting master clones, the HindIII and SalI sites are present so that enzyme pair can be used to liberate the insert -- but beware! There could be HindIII or SalI sites in the insert. See more on the flexibility of using the recombinational cloning approach rather than REs below.
Q. What is the difference between a "discrepancy" and a "mutation"?
A. 'Discrepancy' is a term borrowed from HIP that refers to differences between the actual clone sequence and the target sequence (that is, what the researchers were trying to clone in a specific cloning effort). Discrepancies can result when the clone recovered is an isoform or naturally occurring polymorphic form of the target sequence, or from PCR, replication, or other errors. Be sure to check the insert sequence to be sure that discrepancies that were deemed 'acceptable' to HIP researchers are also acceptable to you.
'Mutations' we define as changes that are known or expected to affect function. We curate an insert as containing a mutation when the insert sequence is a known mutant form (e.g. cloned from a mutant allele) or when the clone was engineered to have a mutation (e.g. in a site-specific mutagenesis effort). Please be aware that there may OR MAY NOT be experimental evidence to support the idea that a particular naturally occurring or engineered mutation results in a constitutively active, inactive, etc. form. And be further cautioned ... neither 'discrepancy' nor 'mutation' is the last word on nucleotide differences between your actual clone and the wild-type form(s). Tags can come from vectors and not be annotated as part of the insert; mutations and deletions may not be clearly annotated or detected by those who shared clones; and recombination or replication errors can change clones over time. DNA sequencing provides an inexpensive and robust means to ask if the clone you received is indeed the clone you requested and that it meets your expectations. Please perform diagnostic tests before investing a lot of time in your experiments!
Q. What's with recombinational cloning (pDNR-Dual, pDONR201, pDONR221, etc. vectors)?
A. Most clones generated at HIP and shared with the repository are based on successful recombinational cloning methodologies such as the Clontech Creator system (LoxP sites) or the Invitrogen Gateway system (att sties). You can learn more about these approaches at vendors' websites and at the HIP website http://www.hip.harvard.edu (look for information about FLEXGene clones). These flexible systems allow a single sequence-verified ORF ("master" or "donor" clone) to be used to create expression constructs for a variety of different techniques via recombination (few steps) rather than restriction enzyme cloning and ligation (several steps). In general, we keep the master clones in our collection because they give the most flexibility to the largest set of users. But in some cases, we also have expression versions. "Entry" or "acceptor" vectors used in combination with master clones to create expression constructs are available from a number of different sources, including Clontech and Invitrogen. Please visit their websites to learn more.
Q. Do HIP cDNA/ORF clones have 5' or 3' UTRs?
A. No. The majority of HIP clone collections (including human, yeast, and more) come from projects in which only the open reading frames (ORFs) were cloned.
Q. Can I get help identifying a large sub-group of clones bioinformatically?
A. Yes. Bioinformaticists at our host institution, HIP, may be willing to collaborate with you to identify specific sub-groups of clones that share some property (biochemical function, sub-cellular localization, up-regulated in a tissue tested by microarray, etc.). Please contact us to initiate this kind of collaborative bioinformatics-based work with bioinformaticists at HIP. Requests are reviewed and accepted on a case-by-case basis. Please note that we make some bioinformatically organized groups of clones available for view and request on the "clone collections" page (for example, human kinase collections and the BC1000 genes associated with breast cancer).
Q. Who should I cite if my work with a clone requested via PlasmID results in publication?
A. The people who put in the hard work to make the clone and any appropriate references should be cited! You should be able to find this information on the clone detail page (click on the CloneID to get there). Look for clone authors and PubMed IDs (vectors can also have associated authors and PubMed IDs).