The overall aim of the Molecular and Cellular Analytical (MCA) core is to support the investigation of human and non-human metabolism from a cellular/molecular perspective. The core was recently restructured to focus on investigation in three areas:
1) Lipidomics and mass spectrometry
2) Bioinformatic analysis of RNAseq data
3) Mitochondrial respiration.
This is a new core being supported by the NORC based on feedback from NORC members on campus. This core grew from the LC/MS and GC/MS analytical capabilities of the Bergman laboratory. We offer analytical services, as well as expertise in interpretation of lipidomic data.
The NORC Lipidomics/mass spectrometry core can quantitatively analyze the following lipids from plasma as well as cells and tissues (muscle, heart, liver, bone):
– Triglyceride species (number of carbons, number of double bonds)
– Diacylglycerol isomers (1,2- vs 1,3-) and species (20+ and growing)
– Dihydroceramide and ceramide species
– Glucosylceramide and lactosylceramide species
– Sphingosine, sphingosine-1-phosphate, ceramide phosphate species
– Sphingomyelin species
– Acyl-carnitine species
– Phosphatidic Acid and Lysophosphatidic Acid species
– Free fatty acid species
Dr. Bergman has been performing GC/MS analysis for his research as well as collaborative projects since 2004. They analyze plasma samples for concentration and enrichment of:
– Free fatty acids
RNAseq bioinformatic pipeline
Next-Gen Sequencing. Our purpose is to provide existing members the Nutrition and Obesity Research Center and researchers at the University of Colorado Anschutz Campus with a consolidated workflow for the management, processing, and biological interpretation of unbiased RNA sequencing gene expression data.
|Metabolic Core||Genomics Core||Global Expression Analysis Service|
|Tissue Processing & RNA Isolation||Library Preparation & Sequencing||Computational Processing||Biological Meaning & Intepretation|
|2 - 4 hours (sample dependent)||1 - 3 weeks (volume dependent)||2 - 5 days (volume depenedent)||2 - 4 hours (upload data, download lists)|
Basics of the Service. We process high resolution RNA sequencing data (FastQ) and implement state-of-the-art computational and bioinformatics methods to supply the end user with statistically significant genes, annotated gene lists, canonical pathways, putative upstream regulators, disease states, gene interaction networks, and biological meaning specific to their research question.
Previous Experience. Drs. Rudolph and Jones (previous director of the Bioinformatics Core for the Cancer Center (2012-2017) have nearly two decades each of global mRNA expression analysis experience. We have a well-established and comprehensive pipeline to quantify significant and meaningful gene expression changes present in your RNA sequencing experiments.
For more information or to schedule a brief project consultation, contact:
Michael Rudolph, Ph.D.
Assistant Professor | Division of Endocrinology, Metabolism & Diabetes
University of Colorado Denver | Center for Women’s Health Research
Associate Director Nutrition and Obesity Research Bioinformatics Core
The Mitochondrial function sub core of the MCA provides services for the comprehensive measurement of mitochondrial function and cellular bioenergetics for both academic and industry users. The core is equipped with a XF96 Seahorse Extracellular Flux Analyzer, two Oroboros O2k Respirometers, and a pair of Strathkelvin Respirometers to assess mitochondrial function via multiple techniques. Measurements can be performed on a host of biological samples including cultured/primary cells, permeabilized fibers or cells, and or isolated mitochondria.
• Respirometry: Extracellular Flux Analyzers are available for respirometry assays in intact cells, permeabilized cells, and isolated mitochondria. These assays can be used to quantify mitochondrial ATP production, maximal capacity of the respiratory chain and the level of uncoupling.
• Training/Consultation: Training is routinely provided for use of the Seahorse XF96 Extracellular Flux Analyzer and the Oroboros O2k systems. Guidance on study design, method development, troubleshooting technical problems, and data analysis and interpretation can be provided for end users.
• One XF96 Seahorse Extracellular Flux Analyzer
• Two Oroboros O2k Respirometers
• Two Strathkelvin Respirometers
• Staff to provide technical training on instrumentation, and guidance designing assays, troubleshooting, analyzing data, and interpreting results