Cores Newsletter October 2024

MESSAGE FROM THE DIRECTOR

Dear colleagues,

As we move into the fall quarter, I’m pleased to share a few highlights and upcoming activities that are relevant to our core facilities.

First, we’d like to give a warm welcome to the new Chief Administrative Officer of the Genome Center, Kyle Summers, who started on October 1st. Kyle brings a wealth of experience from his previous roles in the College of Agricultural and Environmental Sciences, and we’re excited to have him on board as he steps into the shoes of Ernie, who will be sticking around for a period of time to ensure a smooth transition.

Second, I’m pleased to announce that Dr. Jean Challacombe has accepted our offer to be the new Director of the Bioinformatics Core. Dr. Jessie Li, who has served as Interim Bioinformatics Core Director for the past three years, has decided to focus on her other contributions to the core, and we are deeply grateful for her outstanding leadership and service. Jessie will continue her valuable work in the core, while we finalize Jean’s appointment, with her anticipated start in January 2025.

On the infrastructure side, we are discussing plans for the future of our HPC computing resources and exploring the best ways to support the needs of the Genome Center cores and everyone in the GC. We are also in discussions about acquiring instrumentation for hybridization-based spatial transcriptomics, so please let me or the DNA Core know if this is of interest to your work.

We’re also excited about the upcoming Halloween Symposium—thanks to Jeannette Martins, Oliver Fiehn, and the metabolomics group for taking the lead. We have broadened the type of presentations to include short videos, and we encourage everyone to participate in the festivities, costumes, and all!

Thanks to all of you for your hard work and continued contributions to our vibrant core facilities community. We look forward to seeing you at upcoming events.

Blake Meyers

Director, UC Davis Genome Center

UPCOMING COURSES

West Coast Metabolomics Center (Metabolomics Core)

Join us for Bits & Bites 2024 — a flexible learning experience tailored for busy researchers seeking condensed yet impactful sessions. Now in its 4th year, this series continues to bridge the gap for those unable to commit to 1- or 2-week intensive courses. Craft your learning experience by selecting individual Bites à la carte or curate a comprehensive journey by mixing and matching courses for a fully immersive and well-rounded learning adventure.

Remaining Bites of 2024:

See how to register here
If you have questions email: Jeannette Martins, jmartins@ucdavis.edu

Click here to find out more from the WCMC (Metabolomics Core)

Bioinformatics Core

Intro to Python for Bioinformatics

November 18, 20, and 22 from 2-5 pm

This five-part workshop will teach the fundamentals of programming to begin the analysis of bioinformatics data using Python. We will start from the basic building blocks of programming and progress to using simple Python packages for applied bioinformatics analysis.

Single Cell RNA-Seq Analysis

December 9 – 11, 9am – 5pm

This three-day workshop covers experimental design, data generation, and analysis of single cell RNA sequencing data. Participants will explore a single cell experiment using the command line and R, create and modify workflows, and diagnose and treat problematic data utilizing high-performance computing services. The primary packages used for analysis will be 10x software for sequence reads to counts, and the R package Seurat for downstream analysis.

Click here to find out more from the Bioinformatics Core

NEWS FROM THE CORES

UC Davis's New Research Core Directory - Now Live!

Launched this month, UC Davis Office of Research now offers a comprehensive directory of over 70 cores and facilities with more than 450 resources and services to support biological and medical sciences, engineering, agriculture, environmental sciences, social sciences, and the humanities.

Click here to find the Research Core Directory

West Coast Metabolomics Center (Metabolomics Core)

Upcoming Guest Lecture: Hybrid, Double Feature!

The West Coast Metabolomics Center is excited to present a hybrid guest lecture featuring Dr. Ching-Hua Kuo from National Taiwan University and Dr. Doug Worsnop from Aerodyne Research.

Date: November 6, 2024

Time: 10:00 AM - 12:00 PM PT

Location: GBSF Auditorium, UC Davis (In-person)

Zoom: Virtual attendance option available!

Speakers & Topics:

Dr. Ching-Hua Kuo – Mass-Based Methods for Metabolomics and Lipidomics Studies with Clinical Applications
Dr. Doug Worsnop – Targeted Detection of Highly Oxygenated Organic Molecules (HOM) that Condense into Aerosol Particles

Don’t miss this opportunity to engage with groundbreaking research! Join us in person or online via Zoom.

Proteomics Core

High Throughput Proteomics!

Did you know the Proteomics Core can do some seriously fast high-throughput proteomics? Like analyzing 200 samples a day fast.

For example, on Oct 1, 2024, we ran 100 Sparrow (Zonotrichia albicollis) plasma samples that were analyzed using our Bruker timsTOF HT mass spectrometer. All samples were completed in just over 24 hours using our 7-min LC-MS/MS method!

What do you get with our fast service:

Depending on the sample, GPU-based real-time data analysis can also be done while the samples are being acquired for even faster turnaround.
With plasma samples analyzed this fast, we can quantify about 300 proteins per sample.
With cell lysate samples, we can quantify about 2-5k proteins in 7 minutes with over 4 orders of magnitude.
Sample prep can also be automated using magnetic bead processing on a King Fisher for a total time of about 2-3 days from lysates/biofluids to results per 100 samples.

Visit the Proteomics Core's Website

UC Davis Genome Center

451 Health Sciences Dr., Davis, CA 95616

Phone: (530) 752-9654

Don't forget to check out the following Core facilities at the Genome Center:

West Coast Metabolomics Center

Bioinformatics Core

Proteomics Core

DNA Technology & Expression Analysis Cores

Tilling Core