Omics Facility Core

Omics Facility Core

The OFC provides quantitation of toxicant exposures, and the subsequent effects on the proteome and genome, enabling investigators to determine how and where toxicants act.

Determining the exposure to, and effects of, environmental toxicants and the sites and modes of toxicant actions requires a multimethod approach. Combined with data obtained by the Cellular Imaging Facility Core, biochemical assays, and analysis provided by the Translational Research Support Core (TRSC), the OFC aims to advance Center member research. The OFC encompasses a wide range of techniques from routine sample preparation to state-of-the-art chromatography separation, mass spectrometry, and sequencing technologies. The OFC Co-Directors are here to guide and assist Center members with grant proposals, experimental design, sample and data acquisition, data analysis, and dissemination through methods of figure generation using equipment and expertise beyond the scope of their individual Center member laboratories. The OFC also provides more in-depth services including assay development, statistical analysis through the TRSC, and access to self-service instrumentation.

The Omics Facility Core is composed of three labs to support Center members Omics research needs:

  1. An exposomic lab providing services to quantitate toxicants of relevance to the Southwest including inorganics such as metals (arsenic, lead, and mercury), and organics such as polyfluoroalkyl (PFAS) compounds, and industrial chemicals (trichloroethylene) from diverse matrices such as water, air, dust, bodily tissues, and plants;
  2. The proteomics lab providing protein identification, mapping post-translational modifications, disulfide linkage characterization, peptide sequencing, and biomarker quantitation;
  3. A genomics lab providing next-gen DNA sequencing (NGS) of whole genomes, exomes, and transcriptomes (RNA-seq), real time RT-PCR, genotyping, fragment analysis, and Sanger sequencing. Finally, epigenomic and metabolomic services including analysis of histone protein modifications, DNA methylation, and quantitation of toxicant metabolites (e.g., methylarsonic acid) are distributed across the three Omics laboratories based on the analyte and expertise required.

The OFC provides state-of-the-art mass spectrometry, sequencing, and fragment analysis instrumentation to generate exposomic, metabolomic, proteomic, genomic and epigenomic data. The OFC Co-Directors seek to apply their 60 years of collective expertise to provide multimethod approaches that drive research forward through overlapping analyses between the three Omics labs. Serving Center members goes beyond simply analyzing samples and returning raw data. The OFC Co-Directors seek to expand members’ vision of future research ambitions through expert consultation on analytic approaches of which members may not be aware. In addition, the Co-Directors provide advice on study design in consultation with the Translational Research Support Core, consult on logistics, perform initial pilot tests, and advise on budget management before studies begin. Lastly, through their respective experience and expertise, the Co-Directors consult with individual Members after experiments are complete and throughout the dissemination process to ensure quality control of samples and results, perform data analysis and generate figures, and provide interpretation of results. Contact one of the Co-Directors below to get started with achieving your research goals.

Utilizing the Arizona Laboratory for Emerging Contaminants

Exposomic analysis is provided in a laboratory to analytical chemistry of a variety of compounds and chemicals. Those relevant to environmental research within the SWEHSC include:

  • Metals. Trace: (Be, Al, Mn, Ni, Cu, Zn, Mo, Ag, Cd, Sn, Sb, Ba, Pb); Toxic: (As, Pb, Hg, Cd, Al)
  • Inorganic Measurements. Major anions: (Fl-, Cl-, NO2-, Br-, NO3-, PO43-, SO42- ); Major cations: (K+, Ca2+, Na+, Mg2+).
  • Organic Measurements. Pesticides: Atrazine, simazine, prometon, carbaryl, chloropyrifos, DEET; Surfactants: Nonylphenol; PFAS, Perfluorinated compounds (PFAS/PFAC): PFOS, PFOA, PFBS, PFNA, PFHxS, GenX; Pharmaceuticals: Antibiotics, hormones, Industrial chemicals, TMAH, NMP, azoles.
  • Complex Matrices. Water: groundwater, effluent/influent, industrial discharge; Biological: blood, serum, tissues; Environmental: soils, plant matter, biochars, biosolids, and mine tailings.
  • Elemental Measurements. Carbon: Total carbon, organic/inorganic carbon; Nitrogen: Total nitrogen, liquid and solid samples; Sulfur: Total sulfur, solid samples.
  • Water Quality: pH, Conductivity, Metals, Nutrients.

The Exposomic lab instrumentation relevant to SWEHSC research needs includes:

  • Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS): consists of a Quattro Premier XE tandem mass spectrometer from Waters-Micromass and an Acquity Ultra performance (UP) LC.
  • Liquid Chromatography Tandem Mass Spectrometry (LC[QToF]MSMS): The LCMSMS TripleTOF 5600 (quadrupole-Time of flight) tandem mass spectrometer from ABSciex is attached to an Agilent 1260 Infinity HPLC; together they are configured for ESI-LC-MSMS.
  • Gas Chromatography Tandem Mass Spectrometer (GC-MS/MS): is provided by a Quattro micro tandem mass spectrometer 7890A gas chromatograph with a 7683 automatic liquid sampler.
  • UV-Vis/Fluorescence Spectrophotometry: Aqualog Benchtop Fluorometer capable of simultaneously measuring both absorbance spectra and fluorescence Excitation-Emission Matrices.
  • Size Exclusion Chromatography/Asymmetric Field Flow Fractionation-Multi-angle Light Scattering (SEC/AFFF-MALS): This instrument uses liquid chromatographic separation for characterization of mobile particulates in the sub-micrometer range.
  • Ion Chromatography: Thermo Scientific Dionex ICS-6000 HPIC system for the analysis of inorganic anions in environmental samples as it can determine multiple anions in a single analysis.
  • Sample extraction: AT SPE Workstations which can process up to six large volume liquid samples in parallel for further analysis by LCMSMS, GCMSMS, ion chromatography, ICPMS or other techniques.

This resource leverages ALEC, an existing core analytical facility at UA, which is dedicated to providing the analytical capabilities and technical expertise required to detect and quantify small contaminant molecules (organic and inorganic) in complex matrices including biological fluids, tissue, water, air, soil, sediment, and biomass.

Laboratory instrumentation in ALEC is maintained by a combination of funding sources including NSF, NIH, DoE, and the State of Arizona. Principal methods involve off-line or on-line separations followed by mass spectrometric detection. Instruments found in ALEC include:

  • Inductively Coupled Plasma Mass Spectrometers (ICP-MS)
  • Liquid Chromatography Tandem Mass Spectrometers (LC-MS/MS)
  • Gas Chromatography Tandem Mass Spectrometer (GC-MS/MS)
  • UV-Vis/Fluorescence Spectrophotometer
  • Size Exclusion Chromatography/Asymmetric Field Flow Fractionation-Multi-angle Light Scattering (SEC/AFFF-MALS)
  • X-ray Fluorescence (XRF) Spectrometry
  • CNS Analyzer
  • Ion Chromatography
  • Carbon/Nitrogen Analyzer
  • Sample prep equipment - Solid Phase Extraction Workstation, Microwave Digestion

For additional information about ALEC, see the lab website at https://www.alec.arizona.edu/

Consultation:

Complex chemical analysis is best begun with a conversation about the researcher's specific needs. This allows our expertise to consider the intricacies of the project and to suggest the most appropriate steps. Working with us before submitting your samples ensures the best possible research outcomes.

For a consultation, please contact the ALEC Director, Jon Chorover, PhD, by calling (520) 626-5635 or click here to send him an email

Personnel

The ALEC Resource is Directed by Jon Chorover, PhD, and includes two full-time research scientists dedicated to assisting SWEHSC researchers to access the full range of analytical capabilities. Leif Abrell, PhD, oversees organic mass spectrometric analyses (LC-MS/MS, GC-MS/MS, LC-QToF-MS), whereas Mary Kay Amistadi, MS, is in charge of inorganic mass spectrometry (ICP-MS, LC-ICP-MS). These individuals train frequent users or perform analyses on a cost-recovery basis.

Utilizing the RII Analytical & Biological Mass Spectrometry Core

The Proteomics lab provides a broad range of mass spectrometry-based services using state-of-the-art instrumentation and its expertise for proteomics-based research. The Proteomics lab has several high-performance and state-of-the-art MS instruments equipped with electrospray (ESI) and/or matrix-assisted laser desorption/ionization (MALDI) methods. In addition, high-resolution and high mass-accuracy analyses are available for both ESI and MALDI ionization. LC/MS and LC/MS/MS (nano-LC, micro-LC, analytical-LC, and preparative LC) are offered for proteomics and other sample types. Proteomics services relevant to SWEHSC member research include:

  • Protein ID from gel bands or solution isolates.
  • Protein ID from complex mixtures – immunoprecipitation and affinity experiments.
  • PTM characterization – ID and mapping of post-translational modifications such as phosphorylation, acetylation, GlcNAc glycosylation, and ubiquitination.
  • Phosphopeptide enrichment – Immobilized Metal Affinity Chromatography (IMAC), TiO2 techniques.
  • Intact protein analysis – Protein mass determination, truncated proteins, and Top-Down sequencing.
  • Disulfide linkage characterization – mapping cysteine-cysteine disulfide bonds.
  • Peptide sequencing – de novo sequencing.
  • Protein quantification and expression – quantification by isotopically-labeled peptides.

Essential protein tools are also available for protein and peptide purification and protein fractionation, such as FPLC, HPLC, ion and gel filtration chromatography, and gel electrophoresis (1D and 2D). Finally, the recently upgraded Biacore T200 SPR system enables SWEHSC investigators to determine real time label-free kinetics, affinity, and concentrations of interacting biomolecules. The available Proteomics instrumentation includes:

  • Orbitrap Exploris 480 LC-MS/MS system. Next generation advanced high resolution accurate mass Quadrupole-Orbitrap MS for quantitative liquid chromatography-mass spectrometry (LC-MS).
  • solariX 9.4T FTICR LC-MS/MS system. The Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry instrument is primarily dedicated to experiments that require high mass accuracy including PTM analysis, intact protein analysis, and matrix-assisted laser desorption/ionization (MALDI-MS) Imaging (Imaging Mass Spectrometry or Tissue Imaging) of proteins and peptides.
  • ALTIS LC-MS/MS system (Thermo Scientific): The Altis is coupled with Vanquish Duo UPLC System with improved Active Ion Management (AIM™).
  • Q Exactive Plus LC-MS/MS system (Thermo Scientific): A hybrid quadrupole/Orbitrap instrument uses advanced technology to deliver low femtomole sensitivity.
  • Spectro XEPOS X-ray Fluorescence (XRF) Spectrometry: The Spectro XEPOS is useful to assess composition of major and trace elements in solid sample matrices.

  • Q Exactive Plus (Thermo); 2016 University of Arizona purchase; Dionex Nano- HPLC, nanoESI source (Thermo), HCD, Deep and Greater Proteomic Profiling
  • Q Exactive Plus (Thermo); 2016 University of Arizona purchase; Dionex Vantage HPLC, ESI source (Thermo), HCD, Lipid analysis
  • LTQ Orbitrap Velos (Thermo); 2009 NIH NCRR HEI; Proxeon Nano- HPLC, ESI source (Advion), CID, ETD; Proteomic Profiling, PTM identification
  • 9.4t solariX 2XR FTMS (Bruker); 2018 University of Arizona purchase HEI; ESI, nano-ESI, MALDI; CID, ECD, ETD, SORI, IRMPD; high-resolution MS
  • AmaZon 3D Ion Trap (Bruker); 2016 University of Arizona purchase; small molecule rapid MS analysis
  • Autoflex Speed MALDI-TOF (Bruker); 2016 University of Arizona purchase; high throughput MS measurements of polymers, and whole proteins
  • Gel separation and analyses: 1D and 2D gel stations.
  • Off-line LC separation: AKTA FPLC; Michrom Paradigm LC
  • Orbitrap Exploris 480 (Thermo couple with Vanquish Duo HPLC and UHPLC System: 2020 University of Arizona purchase; Next Generation advanced high resolution accurate mass Quadrupole-Orbitrap MS – high performance and throughput for metabolite and lipid analysis.
  • Shimadzu UHPLC-MS; analytical system
  • Shimadzu LCMS; prep purification system
  • Shimadzu GCMS
  • Michrom BioResources, Fraction Collector

Utilizing the RII University of Arizona Genetics Core

The OFC Genomics lab provides state-of-the-art genomic analysis resources and services including a CLIA/CAP certified laboratory for high complexity laboratory testing. In addition, the Genomics core provides novel bioinformatics pipelines for clinical and research purposes designed to integrate UA high-throughput computing for use in analyzing large genomic data sets. Genomics services of relevance to SWEHSC research include:

  • RNA-Seq: Whole transcriptome sequencing and expression profiling with sample barcoding, multiplexing, and data analysis. Large RNA-seq projects can be submitted to an Illumina NovaSeq.
  • DNA-Seq: Both de novo and reference genomes with sample processing starting from DNA extraction through library preparation and sequencing including metagenomic analysis of microbiomes. Sample processing includes unique protocols such as CHIPseq, exome sequencing, amplicon enrichment, and custom library types.
  • Real-Time PCR: Training and access, as well as full service, for genotyping, mutation analysis, gene expression, and custom tests such as measuring epigenetic biomarkers.
  • SNP Genotyping: The Agena MassARRAY, the leading technology for SNP genotyping for sub-whole genome study applications, is used for fine mapping and validation studies.
  • TaqMan expression and genotyping: SNP and gene expression analysis pre-validated probe sets in 96-well and 384-well formats.
  • Sanger Sequencing: Single sample and high volume (96-well plate) Sanger sequencing using the Applied Biosystems 3730 DNA Analyzer. Researchers may expect 600- 800 bases of reliable sequence.
  • Authentication/identification genotyping: Human cell line authentication, transgenic mouse genotyping, STR analysis and custom PCR assays for a variety of organisms and study models.
  • DNA Methylation Analysis: Both NGS technologies, real-time PCR, and the Sequenom MassARRAY system are offered to perform epigenomic analysis of DNA methylation.

The Genomics lab instrumentation includes:

  • Illumina NextSeq500, MiSeq, and sample submission to an Illumina NovaSeq for high-throughput sequencing paired with an Opentrons Library Preparation System.
  • Agena MassARRAY system for high-throughput SNP genotyping.
  • NanoString nCounter Analysis System for digital, single molecule analysis of expression and mutation.
  • ABI 3730 DNA analyzers for low and high throughput Sanger sequencing.
  • ABI 7900 Quantitative/Real Time PCR instruments for 96- and 384-well reactions.
  • KingFisher FLEX Magnetic Isolation Platform and Beckman Biomek FX/NX for automated liquid handling in sample preparation, library preparation, and molecular barcoding.
  • Agilent Bioanalyzer, Qubit fluorimeter, and NanoDrop spectrophotometer for sample QA/QC.

Sequencing:

  • Ion Torrent PGM 314: 0.1 Gbase (small panels, bacterial sequencing)
  • Ion Torrent PGM 316: 0.3 Gbase (large panels, multiplexed samples)
  • Ion Torrent PGM 318: 1 Gbase (large panels, multiplexed samples
  • Ion Torrent Proton 1: 10 Gbase (exome, RNA-seq, Chip-seq)

Microarray:

  • Affymetrix GeneChip platform including 7G upgraded 3000 laser scanner, hybridization oven, and two fluidics stations

PCR/RT-PCR:

  • ABI 7500 Sequence Detection System

Sample quality control:

  • Agilent Bioanalyzer 2100 system
  • Nanodrop 2000 Spectrophotometer
  • Qubit 3.0 fluorimeter