Getting Started
It's important to understand how the core facility works in order to derive full benefit from us. The below information summarizes our policies and procedures, please read carefully and if you have any questions or concerns, contact us.
Billing
All users who wish to access core facility services and equipment need to establish a Genome Center account, typically in the name of the laboratory principal investigator. Once set up, this account is good forever and can be used for all five GC cores. Instructions for setting up an account are available on the log in page. The log in site can also be reached from any of our facility web pages through the box on the left hand side of the page. This log in page will also be your portal for acquiring data. When setting up an account, all individuals in a lab likely to generate data in the core should be listed. A folder is generated on our web server for each entered individual, and this will function as a data depository (more details in the next section). Please read the instructions for setting up a new account carefully, in particular the requirements for the appropriate billing information. UC Davis users must have a DaFIS account number; sub accounts are not required but can be specified. Other UC campuses will use different numbers, as shown in this downloadable list of account string information (your financial person will know more). Non UC users, both non-profit and for-profit organizations, should set up a PO following instructions available here.
Charges are applied to all samples regardless of the outcome of the experiment. The only exception is when a clear failure of instrumentation or sample handling on our part takes place.
Data Storage and Distribution
The core uses two web interfaces to distribute data. One is specific to output from the Illumina Genome Analyzer sequencers, and is described in detail on our sequencing web site. Briefly, current storage policies for sequencing data are that we will store images for two months and text based data for six months, after which charges will be levied (see the sequencing web site for details). The other web interface, accessed through the log in box on the left hand side of this and every core web page, is used for all other downloadable data generated in the core. Data distribution on flash drives is discouraged. Data on this web server is stored for six months free of charge. Following that, no charges are applied but the data may be deleted at any time. You will not necessarily have any warning when this is about to occur. It is recommended you immediately download all your data, and verify its integrity in case the files get corrupted in compression or during transfer. To enable transfer, multiple data files are compressed into a single archive (we zip by default but can rar by request), and certain file name restrictions apply (no spaces, weird characters, etc.--just like the old days). We can easily check from the core whether this data distribution portal is working correctly, so please ask if you want to see the procedure or if you're having any problem
Scheduling
Instrument use in the core ebbs and flows. It is difficult to predict more than a couple of weeks in advance what the turnaround time on a given project will be. In contrast, once samples are dropped off we can typically (important qualifier) give a pretty good estimate of when the first data will be available. We do recommend having early discussions on scheduling, because we don't maintain a stock of many of the materials we use and may need to place orders for your project.
Equipment & Training
An important part of the core's mission is to provide access to equiment and techniques that will advance your research. Equipment available through the core is listed in the home page services menu, and its use is detailed at this site. For information about workshops and other technical training opportunities, subscribe to our bulletin by emailing cmnicolet@ucdavis.edu. Workshop dates are always posted on the core home page right away as well.
Bulletins
Core facility bulletins are peridocially distributed letting you know what's new in the core, what instrument platform improvements are available, information about upcoming workshops and technology related events, and other news relevant to clients (real and desired). To subscribe contact cmnicolet@ucdavis.edu.
Research Support
The core is happy to provide written materials to augment your research efforts. This can include support letters to granting institutions listing available facility resources, details on technical support core personnel can provide, and estimated budget figures for particular research projects. We can also contribute Materials and Methods information for manuscripts that include experiments done in the core. Naturally, we always appreciate acknowledgement in such publications and ask you let us know so we can keep the information in our scrapbook.
Seed Grants
Roughly twice a year the Genome Center issues calls for small pilot proposals funded through each core. These grants award up to 2,000 dollars to spend at any of the cores, and it is also possible to apply for multiple grants at multiple cores. Information on the call is distributed through the facility bulletin and is posted on the core home page and the Genome Center home page.
Projects
In addition to the typical "per sample" fee based system, the core offers a project based recharge system. The project based model is more of an R & D approach in which the researcher pays for access to core technology and expertise in an attempt to achieve a particular research goal. Fees are deposited in agreed-upon lump sums and the core undertakes the project with no guarantees of success (but with high scientific impact if the goals are realized).
Authorship & Acknowledgement
Most of the technologies utilized in the core are scientifically complex and expensive. It is expected that detailed conversations will take place as a matter of course between users and facility personnel at the outset and throughout projects. This does not warrant authorship but we love to see ourselves listed gratefully in the Acknowledgements section when your data is published (please pass along the citation in case we miss it). If extra effort is taken by us along the way, particularly in research where substantial intellectual and technical input is provided, we feel it is appropriate for the researcher to provide authorship to involved facility personnel. This is clearly a gray area in any scientific setting, we all have topical war stories, and because fees are involved it's even grayer (sorry, we can't exchange service for authorship). Just remember that the cheerful professionals that help you out also have resumes, come up for performance reviews, etc. and citations are important additions to their cv. We will attempt to intitate discussions on this early in a project if we feel it's relevant, and basically trust you to do the right thing.
Disclaimer
Reagents, services, and data provided through the Genome Center Expression Analysis Facility are intended for research use only. They are not intended for use in diagnostic or other medical procedures.