CORE FACILITIES
GENETIC/GENOMIC CORE
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.
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.