DNA Technologies & Expression Analysis Core
Core Manager: Dr. Lutz Froenicke
Lab: 530-754-9143 / Fax: 530-754-9658
Set up a PPMS account here (instructions here)
The DNA Technologies and Expression Analysis Core offers high-throughput and custom sequencing, genotyping, and microarray services, as well as trainings and consultations. The lab is a designated UC Davis Campus Research Core Facility.
The core offers the three complementary Next Generation Sequencing (NGS) technologies: Illumina sequencing, and PacBio and Nanopore (long read) sequencing, providing the full spectrum of sequencing options and a wide range of library preparation services for all platforms. Genotyping is performed by sequencing (targeted sequencing and reduced-representation sequencing) as well as on the Fluidigm EP1 and on Illumina Infinium arrays. Gene expression analysis is carried out by RNA-seq on HiSeq, NextSeq, and NovaSeq sequencers. Single-cell transcriptome (high-throughput single-cell gene expression profiling) and genome analyses (linked-read whole genome sequencing) are enabled by our 10X Genomics Chromium System. The core offers annual Illumina and PacBio sequencing library preparation workshops, free consultations on project considerations and experimental design, and custom sequencing library prep solutions. Many of the core’s instruments are available to scientists on campus as shared equipment for a small usage fee after training. We operate a PacBio Sequel, Oxford Nanopore PromethION, Illumina HiSeq 4000, NextSeq, and MiSeq sequencers, and sequence on an Illumina NovaSeq 6000. The sequencers are complemented by liquid handling robots (PerkinElmer’s Sciclone NGS G3, IntegenX’s Apollo, Opentrons OT2), a Covaris E220 sonicator, and a Fluidigm Access Array system for high-throughput sample and sequencing library preparation. The liquid handling robots are employed to minimize sample handling variation and to provide fast turnaround times. The core maintains a data portal allowing users fast access to the data. We offer joint consultations with the neighboring Bioinformatics Core, which provides sequence data analysis and statistical evaluations. Gene expression studies and high-quality de novo genome assemblies are two of the focal points of the Cores.
West Coast Metabolomics Center (Metabolomics Core)
WCMC Technical Director: Dr. Uri Keshet
Lab: 530-754-8553 / Fax: 530-754-8370
Set up a PPMS account here (instructions here)
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 eight LC-MS and seven 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 provides services in univariate and multivariate statistical analysis of data sets, pathway analysis and mapping, partial correlation, and network analysis. We are looking forward to collaborating with you for turning your metabolomic data into biologically significant discoveries!
Proteomics Core
Core Manager: Dr. Brett Phinney
Lab: 530-754-5298 / Fax: 530-754-8370
Set up a PPMS account here (instructions here)
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 Fisher 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.
Bioinformatics Core
Bioinformatics Core transition to UC Davis DataLab
The Genome Center Bioinformatics Core is transitioning its services to UC Davis DataLab beginning July 7, 2026, with the transition continuing through summer 2026.
During this period, the Genome Center and DataLab are working together to maintain continuity for existing bioinformatics projects and to provide a clear path for future support. Existing projects will be reviewed and transitioned in coordination with project teams.
New requests for bioinformatics and data analysis support should be directed to UC Davis DataLab or to [email protected]. DataLab provides support for data-intensive research, including bioinformatics, data analysis, AI and machine learning, statistics, visualization, reproducible workflows, and data management.
The Genome Center is grateful to the Bioinformatics Core staff for more than a decade of service to the UC Davis research community.