Frequently Asked Questions (FAQ)
I would like to obtain a knockout in a tractable
genetic system such as C. elegans but I am unfamiliar to the field. I would
like to know more. Where is a good place to start?
A good primer is Leon Avery's Caenorhabditis elegans WWW
. This contains non-specialist background information, current literature
sources as well as guides to the laboratories and researchers in the field. You
may also wish to investigate the central C. elegans
data repository, Wormbase
How do I make a request?
If you have never done so, you must first set up an account with the Consortium. Setting up an account involves two simple steps. First, click on the link labeled "Create a New Account" that appears on the Consortium Home Page. This link will take you to a form in which you will be asked to provide a username, password and contact information. After you submit this form, you will receive an email asking you to confirm your registration. You must click the link in the confirming email to activate your account. Please note that your browser must accept cookies if you want to order strains from the consortium.
Log on to your account by clicking the "My Account" link on the Consortium home page. After you enter your username and password, you will be taken to your personal home page. To order a target, enter its name in the search box that appears at the top of the page. Click the appropriate link on the search results page. If a strain is available for a given target, you may order it by checking the box adjacent to its listing, and pressing the "Update Cart" button on the order page. To complete your order, follow the instructions on each successive page. You should receive a confirming email once you have completed your order.
Is it acceptable to request a gene knockout from the Consortium and also from other groups with a gene knockout service?
Our goal is to facilitate your research. Therefore, please feel free to make a request with the Consortium, even if you have requested the same knockout from another group.
How long does it take to identify a deletion allele?
The requested target is put into a queue and taken up in turn. We can make no guarantees that a successful knockout of any particular gene will be obtained. Nevertheless, at present, we have the capacity to screen for deletions in 600 targets each month. At our present rate, we recover alleles for about 60 of these. On average, for any given target, it takes six months for the initial recovery of a deletion allele. It then takes additional time to construct a strain that can be released to the investigator.
Once an allele is identified, how long does it take to release a strain?
Alleles that can be maintained in homozygous strains are processed and released in about six weeks after their initial identification. Alleles that must be maintained as heterozygotes take an additional 4-8 weeks to finish because for these we must introduce genetic balancer chromosomes to insure the integrity and stability of the strain.
Where do I get the strain once it is complete?
The consortium does not ship strains to individual investigators. Rather, completed consortium strains are shipped to the C. elegans Genetics Center
(CGC) where they are archived and prepared for distribution to individual labs. Requests to the consortium for existing strains are forwarded automatically to the CGC for processing. The CGC ships most strains within two weeks of their receiving the order.
What guarantees do I have about the nature of a given allele and whether it will be appropriate for my research?
None. We use PCR to detect deletions within a given DNA target interval. Often, we produce alleles that eliminate only a portion of the gene target, or that are in-frame with the coding sequence. Without further evidence, such alleles must be presumed to retain some function. Further, although we try to confine the target to the requested gene, due to the constraints of the protocols, occasionally we must include multiple genes in the interval. Some alleles, therefore, eliminate multiple genes. Such alleles my still be useful.
How many targets can I request?
There are no restrictions on the number of targets you may request. If you have a lot, however, we may prioritize the queue to give other investigators a chance.
I am no longer interested in some of my older requests. Can I remove these from my request list?
Once a gene enters our screening pool, we do not give up on it for any reason. Therefore, we do not provide a mechanism for removing genes from your request list. Once a strain becomes available, you will be notified and given a choice to order it. Of course, you are free to ignore the notification.
A Consortium strain in which I was interested no longer appears on your database. What happened to it?
Strain quality important to us. Occasionally, through our ongoing quality control measures, we identify problems with a strain that lead us to remove it from the distribution list. When a strain is removed, the associated gene target is put back into the screening queue.
We really need the knockout urgently, can our gene prioritized?
Every gene request is important to someone. If you require a gene knocked out urgently we would usually advise that you also make the deletion libraries and screen them yourself. Protocols and guidelines as provided by Gary Moulder and Bob Barstead are available here
Protocols and guidelines as provided by Don Moerman and Mark Edgley are available here
Members of the consortium will of course be willing to give you any additional advice you may need.
What is the cost of obtaining a knockout?
Strains are produced without charge to the investigator. Distribution fees are that of the distributor, the C. elegans Genetics Center . Educational and non-profit organizations are not charged either for processing shipping. Commercial organizations are charged a fee of $100. 00 plus shipping for each strain ordered.
Are there any restrictions on publication of work utilizing the knockout allele?
No. We would ask though that the consortium and the participating group are appropriately acknowledged.
I don't want anyone to know about my knockout target. Can this be kept confidential?
The requestor list is confidential.
Is there a period when the allele will only be available to the initial requestor?
No. The mandate and underlying principle of the consortium is to make the alleles freely available to whoever requests them.
I would like to request a gene to be knocked out. But I do not agree to your terms. How much scope is there for negotiation?
Probably not much. We believe that our terms are fair and act in the best interests of C. elegans research. Also, we already have plenty of requests from people who are agreeable to our terms. However, there may be certain ramifications of our policies that we may not of necessarily anticipated or envisaged. Therefore, we will of course listen and discuss any issues you may wish to raise.
What is the extent of the collaboration?
Unfortunately, we do not have the resources to do any phenotypic analysis of the null alleles.