FAQs

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01 General Information

Please see this page: Getting Started. You will find information on how to set up an account, billing, data storage & distribution, scheduling, equipment & training, bulletins, research support, seed grants, and more.


We are Located in room #1410 of the GBSF building (the Genome Center).

You can use the map link below

Google Maps


We are available every workday from 9 am to 5 pm.
We will be closed on university holidays.  These are listed here:  http://registrar.ucdavis.edu/calendar/holidays.cfm


The building front doors are open in the morning during business hours. After 5 pm please give us a call at 754-9143 and we will come and let you in.
Our usual business hours are weekdays from 9 am to 5 pm.

Please find all the required information on sample submissions and project scheduling on this page http://dnatech.genomecenter.ucdavis.edu/sample-submission-scheduling/.


Please contact the core manager, Lutz Froenicke (lfroenicke@ucdavis.edu)  for pricing questions, quotes, and simple billing questions.

Please contact Jen Stevens from our Business Office Administration for questions about contracts, bank transfers, credit card payments, DaFIS accounts, UC system account strings, and other payment options.

Jen Stevens
Business Office Administration
UC Davis Genome Center
451 Health Sciences Drive, 4303 GBSF
One Shields Avenue
Davis, CA 95616-5270
Ph: 530-754-9648
JenStevens@ucdavis.edu

 


Following analysis of each run, users have access to parsed output through the SLIMS server. A SLIMS account will be created for you on your first run, with information about how to access your account distributed via email (you will receive this email before your actual files are available). The main SLIMS page can be reached here.

You can download all your files from SLIMS with your webbrowser (clicking the links) or better with a download manager (e.g for Firefox https://addons.mozilla.org/en-US/firefox/addon/downthemall/ )

However, it is recommended to download with command line tools.  E.g. by running “wget” (built-in into Unix/Linux/Mac/Cygwin operating sytems, available also for Windows) with a command like the following:
wget -r -nH -nc -np -R index.html*    “http://slims.bioinformatics.ucdavis.edu/Data/Your_RANDOM_STRING/” &
This command will download all files into your current working directory.

You can also archive all your data  with RSYNC by following instructions at
http://wiki.bioinformatics.ucdavis.edu/index.php/Archiving_solexa_data .


  1. Once data are delivered to you, billing information will be entered into the secure web portal at http://cores.genomecenter.ucdavis.edu/
  2. You then have access to pay by credit card immediately. The Genome Center portal will direct you to a secure credit card payment site (please note, no notification is sent at this time, but the invoice is view-able when logged in to your Genome Center account).
  3. Customers are sent an email notification within the first three days of the following month that lets them know their order is available to pay via credit card for 30 days. This email also requests customers notify our business administration: jenstevens@ucdavis.edu (530) 754-9648.
  4. Those that did not pay via credit card during the 30-day period are now manually invoiced and the credit card option in the Cores portal is turned off.
    1. The first days of the month are when invoices are processed by our business administration.
    2. Invoice customers generally receive their invoices after the 15th each month.

This page informs on the data processing included with our sequencing services and bioinformatic analysis options.
This page informs on the data processing options for Infinium genotyping data.

Our neighbors from the Bioinformatics Core provide sequence data analysis, statistical evaluations, consulting, and training to help you get the most out of your data. Please contact us for joint consultations with the Bioinformatics Core staff and also for complete analysis packages including sequencing and bioinformatics (e.g. differential gene expression, variant calling).

 

 


Several pieces of equipment are available for use during normal working hours for a nominal ‘instrument use’ fee. To use the Shared Equipment, first you will need to be trained by Core staff (subject to a ‘training fee’, good for one year). Your PI will need to create an account with the Genome Center and supply a DaFIS # or PO for billing. Visit our login site and follow the instructions for “Creating an Account.” Also visit here to learn more about the Training and Use of Core Facility Equipment. To schedule a time for instrument training, please email the responsible staff member.


Please support us by acknowledging our services in your publications. We have received NIH funding for the purchase of some of our instruments and this support should be mentioned. Please add a sentence like this to your acknowledgments: “The sequencing was carried out at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center, supported by NIH Shared Instrumentation Grant 1S10OD010786-01.”
Acknowledgments like this constitute a big support for future NIH instrumentation grant applications.


We ask you to mention our services in the acknowledgments of your publications.  This will support our applications to instrumentation grants and thus help to improve our services.
Please see the the details here.
If you feel we contributed intellectually to your project it is appropriate for us to share authorship.  If you have any questions please talk to us about it. For a more detailed discussion of authorships when using a core facility please have a look at the ABRF Authorship Guidelines. These are the community standards most core facilities follow when there are questions about authorship.

Seed Grants

Yes, the Genome Center invites proposals for pilot projects that merit support by the Genome Center. These seed grants award up to $2,000 to spend at any of the Cores; it is also possible to apply for grants at multiple Cores to UC Davis labs.  The Genome Center seed grants are available all year round. They are meant to either introduce UC Davis labs to high-throughput sequencing or genotyping methods, or to help establish new methods.  They will fund up to $2000 per project.  Equivalent pilot grants are also available through the Bioinformatics core. Please see: http://dnatech.genomecenter.ucdavis.edu/2014/07/31/2015-genome-center-cores-pilot-grant-program/ . A seed grant application should be about one page long and include an outline of the project including the planned data analysis, a sentence on how the project would fit in with the goals of the GC seed grants,  a listing of the specific services to be provided by our Core, as well as a budget (including an account number in case the costs exceed the grant amount).


The BGI@UCDavis was located in the School of Medicine on the Sacramento campus and did provide sequencing services for large scale sequencing projects up until September 2015. This BGI facility is now closed.  Since our DNA Technologies Core operates the latest generation of sequencers (HiSeq3000/4000),  which offers a 7 times increased throughput compared to the previous generation, our Core is now taking on also large sequencing projects. The DNA Technologies Core is offering all the services previously provided by the BGI@UCDavis. In addition we offer many specialized services and support for custom sequencing projects.


A purchase order (or “PO”)  is only required for customers from outside the UC system.   Please email the POs to both Jen Stevens at our Business Office (JenStevens@ucdavis.edu) and us at dnatech@ucdavis.edu.

A purchase order is a simple  letter from your financial administrators listing the requested services and prices.
It has to include the full contact information of your financial administrators as well as the name and institution of the Principal Investigator (“PI”).
The PO has to state the specific services requested from us – essentially repeating the information provided in quotes from us or from the recharge rate listing from our webpage.
POs should have an ID number on them which your administration can generate according to their preferences.

Please feel free to use your standard PO forms. This purchase order template, with all the required and suggested fields, is a suggestion:  http://dnatech.genomecenter.ucdavis.edu/wp-content/uploads/2016/04/purchase-order-DNATech3_1.doc

Please see this page for more information on POs: http://blog.procurify.com/2013/09/23/all-you-ever-needed-to-know-about-purchase-orders/
We did modify a generic PO template from here: http://www.vertex42.com/ExcelTemplates/excel-purchase-order.html

 


If you are interested in receiving information about new services, workshops and other updates from the DNA Technologies and Expression Analysis cores, please subscribe to the dnatech_news list.  Please use the UC Davis email address, if applicable.  To subscribe to the list, send an email to sympa@ucdavis.edu with the following information in the subject line:

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