Core facilities

Genome Center Core Facilities

Users of the Genome Center Core Services can set up an account which will enable you to use all the core facilities.

 

Bioinformatics Core

Website: http://bioinformatics.ucdavis.edu — Email: bioinformatics.core@ucdavis.edu

Core Manager: Dr. Matt Settles
Core Office: 530-752-2698

The Bioinformatics Core provides expertise and infrastructure for the acquisition, curation, analysis, and distribution of large complex biological datasets, with an emphasis on sequence data. We offer data analysis services, free consultations for grant or project planning, and training aimed at empowering graduate students, post-docs, and PIs to do their own bioinformatics data analysis. Also, we can help you design, install, and maintain your lab’s high performance computing infrastructure, providing stable support even as lab members come and go. Please send us an email or call (530-752-2698) with your questions, or visit our website to find out more about how we can help you.

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DNA Technologies Sequencing Core

Website: http://dnatech.genomecenter.ucdavis.edu/ — Email: dnatech@ucdavis.edu

Core Manager: Dr. Lutz Froenicke
Lab: 530-754-9143, Fax: 530-754-9658

The DNA Technologies Core provides Illumina high-throughput sequencing, PacBio long read sequencing, as well as Fludigm EP1 and Illumina BeadArray high throughput SNP genotyping. The Core further offers many sequencing-associated services such as library preparation and QC, as well as consultations on project design. Downstream analytical options can be coordinated with the Bioinformatics Core.

High throughput DNA sequencing (e.g. whole genome, targeted sequencing, transcriptome, ChIP-seq, metagenome) and variant detection is available using Illumina HiSeq and MiSeq sequencers that generate up to 600 Megabasepairs of sequence each run (HiSeq), with read lengths of up 2 x 300 bp (MiSeq). The PacBio RS instrument generates long reads (up to ~8 Kbp average length and maximum read lengths of more than 20 Kbp).

For SNP genotyping the Fluidigm EP1 platform offers efficient low- to mid-multiplex SNP genotyping at customizable scale.  The Illumina GoldenGate Assay can analyze 384 to 1,536 SNPs/sample, and the Infinium platform can analyze from 7,600 to over 1,000,000 SNPs per genotype. Advice on project design is also available and we have experience in working with data from a diverse range of plant and animal species.

Several items of equipment (Molecular Devices plate reader, Nanodrop, Bioanalyzer, Covaris and Bioruptor sonicators, Caliper SciClone liquid handler, Caliper Gx, Fluidigm Access Array, Fluidigm C1) are available for use by members of the research community after training by Core personnel (for a nominal annual fee).

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Expression Analysis Core

Website: http://genomecenter.ucdavis.edu/expression_analysis — Email: dnatech@ucdavis.edu

Core Manager: Dr. Lutz Froenicke
Lab: 530-754-9143, Fax: 530-754-9658

The Expression Analysis Core offers many RNA-seq options such as ribosomal RNA-depletion, polyA enrichment, strand-specific sequencing, and ultra-low input libraries.  Multi-day RNA-seq library prep workshops are also offered on a regular basis. The Illumina BeadArray gene expression platform is available for expression studies in human and mouse.

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Metabolomics Core

Website: http://metabolomics.ucdavis.edu — Email: metabolomics@ucdavis.edu

Core Manager: Dr. Oliver Fiehn
Lab: 530-754-8553, Fax: 530-754-8370

The metabolomics core provides untargeted and metabolite target analyses for a wide range of biochemical pathways, covering over 1,200 identified metabolites with validated analytical methods and known mass spectra and retention times. The facility utilizes 8 LC-MS and 7 GC-MS instruments with both nominal mass and accurate mass capabilities. The core is happy to engage in project specific method development and implementation.

The core further provide services in univariate and multivariate statistical analysis of data sets, pathway analysis and mapping, partial correlation and network analysis. We are looking forward to collaborate with you for turning your metabolomic data into biologically significant discoveries!

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Proteomics Core

Website: http://proteomics.ucdavis.edu — Email: proteomics@ucdavis.edu

Core Manager: Dr. Brett Phinney
Lab: 530-754-5298, Fax: 530-754-8370

The Proteomics Core provides state-of-the-art analytical proteomic services with particular emphasis on label free quantitative proteomic profiling, the analysis of macromolecular complexes, the post-translational modification of their constituents and standard protein identification from complex protein mixtures.

The Core, has a staff of six individuals including two Ph.D. scientists. For high throughput identification and characterization of proteins and peptides the Core has at its disposal several state of the art LC-MS/MS systems including a new Thermo Scientific Q-Exactive Orbitrap mass spectrometer connected to an EASY nLC II system, a LTQ-FT Ultra hybrid Fourier Transform Ion Cyclotron tandem mass spectrometer connected to a Waters Acuity Ultra High Pressure Nano UPLC, two Thermo Scientific LTQ tandem mass spectrometers connected to a Michrom Paradigm HPLC’s, and a Thermo Scientific TSQ Vantage Triple Quadrupole mass spectrometer for quantitative multiple reaction monitoring (MRM) targeted proteomics experiments. Core personnel can also provide amino acid analysis using one of three Hitachi amino acid analyzers and N-terminal sequencing using one of two N-terminal sequencers if needed.

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TILLING Core

Website: http://tilling.ucdavis.edu/ — Email: genome.tilling@gmail.com

Core Manager: Dr. Luca Comai
Lab: 530-754-1316

The TILLING Core provides mutants for rice, Arabidopsis thaliana, and tomato as well as other species on request. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetic technique that uses chemical mutagenesis to create libraries of mutagenized individuals that are subjected to high-throughput sequencing for discovery of mutations.

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Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

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