FAQ

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.

The PPMS system is used to place orders (Core personnel only), to book shared instruments and schedule trainings.
Use of the PPMS system requires a one-time registration. The same system will be implemented in the near future by many other UCD Core labs.
We recommend submitting your PPMS account request as soon as possible since it will require a (fast) check/approval through our administration. The ‘group’ in PPMS is named after the PI, with other ‘users’ linked to the PI’s account – in general, it will be easier if the PI initiates the first PPMS account request.
Only customers (both the submitter and the PI) can enter financial/billing account information into PPMS; please make sure that the applicable financial account is entered before any submission.

Once the PPMS account is generated and the financial account is registered, please submit samples as described here.  Upon arrival of the samples, the Core staff will enter the order in PPMS where you can review it. You will be notified by an email via PPMS.

To begin using PPMS:

1. Ask your Principal Investigator to set up a lab group and a user account in PPMS here. On the menu bar, click on the Account Creation Request link. The group name has to be the name of the PI; the administrative/financial contact information is required; if possible a default KFS/financial billing account for the group should be entered; each user can add their billing account (or a PO for users outside the UC system) to the group. Non-UC customers wanting to pay by credit card, please leave the financial account information field blank.  You will receive an invoice via email with instructions once your order has been processed.
2. Then submit your personal account request. 
3. Wait to receive the PPMS account confirmation e-mail.
4. Only customers can enter billing account information into PPMS!  Before placing an order or submitting samples, please make sure that the desired KFS/financial billing account # is entered in PPMS (for users from other UCs the same applies to chart strings).
5. For shared instrument users, notify the Core that your account has been created and let us know for which instruments you were trained on previously.  The Core will then grant you user rights on the appropriate systems (instrument calendars) and you can begin making reservations in PPMS.

Please see these FAQ and PPMS account-setup help files for each of three user groups:

• UC Davis Users
• Other UC System Users
• Outside Users (Academic, Non-Profit, and Industry Users)
  

A general PPMS user help guide is available on the start page.
If you encounter any technical issues or have questions about PPMS, please see the PPMS FAQ, or email GCcoreadmin@ucdavis.edu .

Please also see our Getting-Started Guide with other administrative information on working with our Core and the Genome Center.

See this page for all the options: https://dnatech.genomecenter.ucdavis.edu/consultations/

Please pick a time & book your general consultation appointments with the Core director here:  https://dnatechlutz.youcanbook.me/

The Genome Center Cores provide services at three recharge rate scales. The University of California rate scale (UC rates) applies to all projects paid through UC-system accounts. Non-profit/academic rates apply to all other non-profit research including government projects. The industry rates apply to all projects paid from for-profit businesses or institutions.  Please make sure that you have a PPMS account to place requests and to enable invoicing.
Upon arrival of the samples, the Core staff will enter the order in PPMS where you can review it. You will be notified by an email via PPMS.  You will be invoiced after you have received the data.

The invoicing process will vary slightly for UC Davis customers, other UC-system customers, and non-UC customers.

UC Davis customers:

1. Once data are delivered to you, the project billing information will be entered into the secure PPMS system at https://ppms.us/ucdavis/login/?pf=5 , where you can view it.
2. In the first days of a month your UC Davis DaFIS/KFS accounts will be billed processed.
   Please note that the billing date (‘completed’) is recorded and that this is sufficient for expiring grants. The final processing can occur after the deadline (usually up to two months).

Other UC system customers:

1. Once data are delivered to you, the project billing information will be entered
2. into the secure PPMS system at https://ppms.us/ucdavis/login/?pf=5
3. , where you can view it.
4. In the middle of the following month the UC inter-campus transaction system will bill your account via an ITF.

Non UC-customers (academic, non-profit and industry):

1. Once data are delivered to you, the project billing information will be entered into the secure PPMS system at https://ppms.us/ucdavis/login/?pf=5, where you can view it.
2. 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: gccoreadmin@ucdavis.edu (530) 754-9648.
3. 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 15^th each month.

The UCD Genome Center accepts money transfers, credit card, and government purchase card (GPC) payments, etc.

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

Non UC system users, both non-profit and for-profit organizations, can request invoicing (after data delivery) simply by entering the terms “credit card” or “invoice” in the account fields of the submission form. You can also set up a purchase order (a “PO”) beforehand and add the number to your PPMS account.
We require purchase orders only for institutions outside the US.  Please email the POs to our Business Office (gccoreadmin@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

Please see this page with the full contact information.

Lab questions:
Email: DNATECH@UCDAVIS.EDU
Lab phone: 530-754-9143

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Please see this FAQ:  What Information Do You Require About My Project?

To be able to help you quickly with current or recent projects we always need the following information:

• PI name
• Submitter name
• Project ID  (e.g.  HiSeq3421)
• Submission date (even if vague)

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
gccoreadmin@ucdavis.edu

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 lists.

Please always use the UC Davis email address, if applicable.   We will send news of exclusively local interest to the dnatech_local_news list only and not try to not bother other subscribers with these.   The UC Davis users will receive all news.

To subscribe to the lists, UC Davis users should send an email to sympa@ucdavis.edu with the following information in the subject line:

subscribe dnatech_local_news first_name last_name

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To subscribe to the list, all non-UCDavis users should send an email to sympa@ucdavis.edu with the appropriate text in the subject line:

subscribe dnatech_news first_name last_name

Unsubscribe

You can unsubscribe from the list by simply sending an email to sympa@ucdavis.edu with the following information in the subject line:

unsubscribe dnatech_news

or

unsubscribe dnatech_local_news

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 (these is a training fee per person). 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, and to book instruments please use the PPMS system. Please see this page for PPMS information.

Consultations

We can provide better advice on appropriate or optimal sequencing options if you provide us important background information on your project. We suggest using the questions below as a starting point for inquiries.

Information requested for RNA-sequencing projects:

• Which species are you studying (prokaryotic or eukaryotic)?
• From which sample types will the RNA be isolated (e.g. tissues, cell cultures, whole organisms)?
• What is the objective of the study (e.g. differential gene-expression (DGE) study, gene annotation, identification of iso-forms)?
• For differential DGE studies: Are you interested only in gene-level DGE, or do you want to study the expression of the different transcripts of genes? Are you interested in non-coding RNAs?
• Do you expect lowly expressed genes to become important for your study?
• How closely are related (genetically) are the biological replicates?
• Do you expect to induce strong phenotypic changes by the varying treatments?
• What total RNA amounts do you expect to extract from the samples?
• What is the expected integrity of the RNA samples (e.g. RIN-scores)? Do you expect potentially interfering chemicals in the samples (e.g. phytochemicals)?
• How many samples do you want to study? Will the samples be available at the same time?

RNA-seq options are described on two pages: RNA-seq and 3′ Tag-Seq Gene Expression Profiling.

Information requested for DNA-sequencing projects:

• Which species are you studying (prokaryotic or eukaryotic)?
• What type of samples are you going to submit (e.g. genomic DNA, amplicons, metagenomic samples, purified strain or population samples)?
• What is the expected genome size? What genome coverage are you aiming for?
• What is the objective of the study (e.g. SNV variant analysis, genotyping, de novo genome assembly, structural genome variants, metagenomic analysis)?
• For de novo genome assemblies: Are you interested in genic regions or do you require the full genome sequence? Do you require the ordering of the assembly scaffolds?
• What DNA amounts do you expect to extract from the samples?
• What is the expected DNA sample integrity (fragment sizes)? Do you expect potentially interfering chemicals in the samples (e.g. phytochemicals)? What protocol are you using for the DNA isolation?
• How many samples do you want to study?

Most DNA-Seq options are described here.

 In-Progress Project Inquiries

To be able to help you quickly with current or recent projects we always need the following information:

• PI name
• Submitter name
• Project ID  (e.g.  HiSeq3421)
• Submission date (even if vague)

Samples will be stored in the freezer for no longer than one year past the date of submission.  DNA samples and sequencing libraries will be stored in a -20 degree C freezer.  RNA samples are stored in a -80 C freezer. Please arrange for a pickup of your samples in the weeks immediately after data delivery.

We can also return samples to you via FedEx. This requires that we receive a PDF version of a completed shipping label from you using your FedEx account details. Please make sure to check dry-ice shipping for RNA samples when ordering the FedEx shipping label.

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

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).

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 are a big support for future NIH instrumentation grant applications. Thanks in advance!

Most of the technologies used 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. 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, and because fees are involved it’s even grayer. Just remember that the cheerful professionals that help you out also have resumes, come up for performance reviews, and citations are important additions to their CV. We will initiate discussions on this early in a project if we feel it’s relevant. So far everyone has been more than accommodating, so thank you all for that!

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. Only UC Davis labs can be eligible for these grants.

The Genome Center seed grants are available year-round. For the DNA Technologies Core, the seed grant program has two major objectives:

• introduce UC Davis labs to high-throughput sequencing or genotyping methods (applies to labs that have not used our technologies before)
• support the development of new genomic and transcriptomic methods/protocols

A seed grant application should be informal but should be about one page long and include:

• a short introduction on the scientific question being addressed and a short outline of the project
• a sentence on how the project would fit in with at least one of the objectives of the seed grant program
• an outline of the planned data analysis (will there be a qualified analyst and computational resources available ?)
• a listing of the specific services to be provided by our Core
• a budget (including an account number in case the costs exceed the grant amount).

We highly suggest discussing your proposal prior to submission of an application with the core manager. Please see the consultation link on the home page.
After approval of a seed grant, samples have to be submitted within three months, for the project to stay eligible for the seed grant support.  Please understand that funds will be allocated to other projects, if the time frame is exceeded.

Equivalent pilot grants are also available through the Bioinformatics core. Please contact the Bioinformatics Core here: bioinformatics.core@ucdavis.edu.

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.