Center for Hypertension and Precision Medicine

CORE FACILITIES

GENETIC/GENOMIC CORE
The genomic core is maintained by Dr. Xi Cheng and contains equipment required for genotyping, functional assays, mutation detection and positional cloning: StepOnePlus™ 96-well Real-Time PCR System from AB-bio system; digital camera for recording agarose electrophoretograms from Gel logic- 100 imaging system, Kodak. Protean II Xi 2-D Electrophoresis from Bio-Rad; Omega Lum G chemiluminescence/UV-VIS gel and membrane documentation system from Aplegen; Blotcycler automated membrane processor from Precision Biosystems; Applied Biosystems (ABI) 7500Fast qPCR machine; Qiacube from Qiagen-for extraction of RNA, DNA and Protein; TissueLyser LT with 12 tube adaptor from Qiagen; Agilent 2100 Bioanalyzer.                                  

Microbiome Core:
The microbiome core is equipped with an Illumina MiSeq next generation sequencer that can generate 15 Giga bases and enables pooling of 96 samples in a library for metagenomics analysis. The core provides 16S metagenomics services for internal and external users, including DNA extraction, library preparation, sequencing and data analysis from a variety of biological samples (feces, saliva, oral swabs, tissues) of rodent, fish and human origin. After sequencing, data (FASTQ files) is processed and provided to the user in a compressed folder that includes operational taxonomic unit (OUT) summary, diversity analysis, taxa summary, enriched taxa, predicted functional pathways and statistical analyses.  The microbiome core also performs whole genome sequencing for cultured bacteria using Illumina Nextera XT library kit, with as little as 10ng of DNA. For pricing and more information click here: Microbiota/Microbial Community Services.

Other Institutional Resources:

The following resources are available through the George Isaac Laboratory for Cancer Research (GILCR). This laboratory was established following generous funding from the George Isaac family. Under the direction of Dr. Willey, this laboratory harvests expertise and resources from the UT-Promedica community to advance collaborative translational lung cancer research. Major equipment available at the GILCR are: an Ion Torrent PGM System for next generation sequencing, three thermal cyclers for PCR (one of which is an ABI Fast 7500 realtime instrument), three Agilent 2100 Bioanalyzers for microfluidic capillary electrophoresis and analysis of nucleic acids and proteins, six agarose gel electrophoresis units with power supplies, two microcentrifuges, two tissue culture laminar flow hoods, two tissue culture incubators, one fume hood, an inverted microscope with digital camera, balances, a refrigerated tissue culture centrifuge, a Nanodrop spectrophotometer, two refrigerators, two - 30 degree C freezers and one -80 degree C freezer. A Fluidigm Access Array system is available on loan from Fluidigm in the P.I.’s laboratory and a MinION MkI nanopore next generation sequencing device has been delivered to the University of Toledo as a beta test device, and is accessible for this proposed project. Shared resources include FACSAria IIU and FACSCalibur flow cytometers, Abbott m2000 and Life Technologies StepOnePlus real-time PCR instruments, a refrigerated high-speed centrifuge, autoclaves, walk-in cold room, and a dark room with an automated processor.

BIOINFORMATICS CORE

The CHPM Bioinformatics Core is operated and maintained by Dr. Xi Cheng. This core provides the infrastructure for the analysis and visualization of large datasets, with an emphasis on various sequencing data and promotes individual researchers to tap the ever-growing data generated by new research technologies. CHPM has power tools for the analysis and visualization of RNA-Seq, ChIP-Seq, DNA-Seq, and Methyl-Seq data using Strand-NGS software package (V.2.5.1). Strand NGS supports an extensive workflow. The workflow includes various features including standard differential expression analysis, differential splicing analysis, differentially methylated cytosines across samples/target genomic segment, detecting variants (SNPs, MNPs and short InDels), copy number variations, identifying transcription factor binding sites, and identifying histone modification sites using the PICS and MACS peak detection algorithms as well as. It also supports for novel discovery including identifying novel genes and exons and novel splice junctions. It includes the ability to detect variants in the transcriptome, and the ability to detect gene fusion events. Further downstream analysis such as GO, pathway analysis, etc can be performed on the set of interesting genes.

Additional bioinformatic resources are available through the UT Health Science Campus Bioinformatics Computer Lab,  which was developed for both teaching and research purposes. This computer laboratory contains a dual 2.0 GHz G5 processor Macintosh running Mac OS X Tiger, and a 3.0 GHz, 2.5 GB RAM Dell computer running Windows XP. In addition, the lab recently acquired 18 Intel core duo 2.66 GHz iMacs, with 4 GB of RAM, and running a dual-boot OS with Windows XP and Mac OS X Leopard. They are fully networked and thus can be used as a UNIX cluster during off-peak hours. In addition, there are two Linux workstations (16 cores with 2.8 Ghz processors; 128 GB of RAM; 2 TB hard drive) and six modern computers with Internet2 access via the College’s gigabit Ethernet backbone, and has an assortment of software for managing, analyzing and graphically representing data. All the computers are equipped with SAS, SPSS, R, and n-Query program. These computers have access to the Ohio state-wide grid of supercomputer clusters from Ohio Supercomputer Center (OSC), Columbus, OH, and support from the personnel for parallelization of large-scale computations. OSC’s HP-built, Intel® Xeon® processor-based supercomputer, dubbed the Oakley Cluster, can achieve 88 teraflops or, with acceleration from NVIDIA® Tesla™ graphic processing units (GPUs), a total peak performance of 154 teraflops.

BIOCHEMICAL CORE
The biochemical core contains all the standard equipment necessary for all biochemical analysis from tissue/cell culture samples. Polytron- PT3100D tissue homogenizer from Kinematica AG, temperature controlled Sorvall RC-5C Plus Superspeed Centrifuge, NanoDrop 2000 UV-Vis Spectrophotometer from Thermo scientific, SpectraMax spectrophotometric micro plate reader from Molecular Devices and GloMax-96 Microplate Luminometer from Promega. Two laminar flow hoods and two inverted microscope for cell and tissue culture from Leica. ELISA plate shaker; 96-well plate washer; ultracentrifuges; Environ Shaker from Lab-Line; Centrivap Concentrator from Labconco; Gel Dryer from Bio-Rad; WKL 230 Water Cooler from Brinkman; HM550 Cryostat from Thermofisher; Biological Safety Cabinet from Forma Scientific; Heracell 150i Tri-Gas cell culture incubator from Thermo Scientific; Bio-rad TC10 automatic cell counter; Hugo Sachs Elektronik Easy Cell Extraction System Type 803 for isolation of primary cardiac fibroblasts and myocytes via aortic perfusion of whole hearts from Harvard Apparatus. Odyssey Infrared protein detector system: this system provides a highly sensitive and accurate way to quantify immune-detected proteins on blotting membranes. It also has the capability for simultaneous detection and quantification of multiple proteins. 
IMAGING CORE
The core is equipped with a Leica TCS SP5 Laser Scanning Confocal Microscope with a Multi-photon Laser and is located within the University of Toledo's Advanced Microscopy & Imaging Center.  Specifically, the Leica TCS SP5 is equipped with both conventional and high-speed resonance scanners. The Multi-photon laser is attached to an inverted microscope and allows deeper penetration into tissue with less photo-bleaching/damage. Five lasers plus multi-photon excitations are available, producing the following laser excitation lines:  458, 488, 514, 561, 633, and 710-990nm (from the tunable Ti-Sapphire MP laser).  The system is capable of collecting up to 7 colors simultaneously for quantitative confocal image analysis, 3D reconstruction, FRAP and FRET, animation, stereo imaging, single layer projection, time lapse collection, and co-localization analysis.
Last Updated: 1/30/19