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Cores Newsletter April 2024

MESSAGE FROM THE DIRECTOR

I am pleased to join UC Davis and the Genome Center as the new director. First, a big thank you to Richard Michelmore for his many years of outstanding service to the Genome Center, stretching back to its founding. He and his lab members have also been helpful and accommodating to me and my lab members as we’ve moved into the Center and gotten settled. And what a move it has been! You might not have seen as much of me as you might want or expect, but that’s because there are so many tasks to check off the list, ranging from unpacking to new employee matters (for me), to our settling our home (how do you register a new, out-of-state, leased vehicle in California?), to authorizing a new lab on campus, and to even figuring out exactly what the day-to-day of my new job entails. I am thrilled to be back in Davis – it is my third time moving here, as I was at UC Davis both for graduate school and my second postdoc. I look forward to getting to know everyone at the Genome Center, and to building my network across campus so that I can promote the exciting science and technologies of the Genome Center, and continue to grow its impact.

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UPCOMING COURSES

Metabolomics Core

  • International Sessions in Metabolomics & Exposome Studies 2024 on Aug 19-29, 2024. Register here
  • Bits & Bites # 04: Quantification in Metabolomics: Tools for Robustness on May 9, 2024. Register here
  • Bits & Bites #05: Using MS-DIAL to generate accurate comprehensive LC-MS/MS metabolomics datasets on May 23, 2024. Register here


Find more courses from the Metabolomics Core here

Bioinformatics Core

  • Introduction to Python for Bioinformatics on April 29 - May 3, 2024. Register here
  • Introduction to the Command Line for Bioinformatics on June 3 - June 7, 2024, Register here
  • Single Cell RNA-Seq Analysis on June 10 - June 12, 2024. Register here
Find more courses from the Bioinformatics Core here

Proteomics Core

  • 2024 Hands-on Proteomics Short Course on Aug 26-30, 2024. Join the waitlist here
Find more about the 2024 Proteomics Short Course here

NEWS FROM THE CORES

West Coast Metabolomics Center

  • Targeted LC-MS Team Triumphs in Q1 2024! We are thrilled to announce that our esteemed Targeted LC-MS team has made a remarkable comeback, approaching pre-pandemic sample numbers once again! As depicted in the recent data, 2024 marks a significant milestone where resilience and innovation converge. Read more here.
  • Our Targeted Assays:
  • Bile Acids: From Biocrates®, we offer a comprehensive bile acids assay 
  • Oxylipins: The Oxylipins assay is at the forefront of unveiling the roles of these lipid mediators in inflammation, immunity, and cellular signaling. 
  • Steroids: Our steroids assay delineates the multifaceted world of steroid hormones.
  • We work with various samples from human stool, Equine plasma, mouse plasma, mouse stool, mouse liver, rat plasma, bovine cell culture media, etc. Check out what types of samples we've had in Q1 2024, read more here.
Visit our Website

Proteomics Core

  • Need preliminary data for an upcoming NIH grant? We have funding available to generate preliminary data on our NIH S10 funded Thermo Exploris 480 LCMS system. Only restriction is that it be an NIH grant eligible for being a major user on a NIH S10 grant program, these include R01 and other substantial multi-year funding, examples include D,K,P,R and U mechanisms.
  • Join us for our bi-weekly Proteomics Journal club! Located in the GBSF building hosted by the Proteomics core and the Kuletz Lab. All are welcome, even if you don't know what proteomics is! (Spoiler: it's super cool) For information please see registration link here.
Visit our Website

Bioinformatics Core

A recent publication in JCI by Elizaldi et al with the participation from the Bioinformatics Core Interim Director, Jie Li, and Biostatistician Blythe Durbin-Johnson, titled “Chronic SIV-induced neuroinflammation disrupts CCR7+CD4+ T cell immunosurveil-lance in the rhesus macaque brain” uses a combination of single-cell gene expression, single-cell chromatin profiling and spatial transcriptomics to reveal a distinct subset of CCR7+ CD4 T cells resembling lymph node central memory cells and to highlight a role for CCR7+ CD4 T cells in CNS surveillance and their responsiveness to neuroinflamma-tion in chronic SIV infection in macaque.


To read more click here

Visit our Website

DNA Technologies & Expression Analysis Core

  • The lab now supports spatial transcriptomics studies with the 10X Genomics Visium chemistries. Read more here.
  • Element Bio AVITI sequencer has been upgraded and a second AVITI sequencer has been added. Read more here.
  • Highest quality sequencing with UltraQ reagents that will enable sequencing at Q50 improving accuracy by 100 times. Read more here.
  • We are gathering feedback with regards to current and coming technical options regarding cyto-profiling and spatial multi-omics. Read more here.
  • Please contact the Genome Center director Blake Meyers (bcmeyers@ucdavis.edu) and the DNA Tech Core manager (lfroenicke@ucdavis.edu) if you have interest in in situ hybridization based spatial multi-omics or cyto-profiling.
Visit our 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

Yeast One Hybrid Services Core

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