Genomics Services & Training

These facilities function to increase the competitiveness of genomics research at the Oklahoma State University by providing training with access to genome sequencing equipment and bioinformatics software.

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GENOMICS CORE RESOURCE FACILITY

Overall Capabilities

The facility provides service and training for Next Generation Sequencing (NGS) and bioinformatics at all levels. Training is provided through Workshops, Genomics/Informatics curricula, and The Carpentries (based at the OSU Library). The facility also provides consultation for experimental design, projects, and proposal development. A full-time PhD-level specialist is employed to assist researchers.

Major Services and Equipment

• Genome- and Microbiome-level DNA and RNA sequencing using an Illumina NextSeq500 instrument
• Agilent Bravo robotic sequencing library preparations for DNA and RNA
• RNA-seq for differential expression, transcriptomics, and meta-transcriptomics
• Extensive NGS capabilities including microbiomes, eukaryotic targeted (exome) sequencing, & scSEQ.
• Analysis of NGS data outputs (quality control, assembly, annotation, variant detection, etc.)
• Bioinformatics training, scripting, data visualization, and short-format topic-specific workshops
• Big data archival storage
• NCBI Genome Submission Center
• DNA microarray production of custom libraries
• Functional annotation, pathway analysis, and metabolic profiling
• Robotic nanoliter to milliliter liquid handling

Multi-user equipment

• Agilent BravoA NGS library preparation liquid handling system
• NanoDropII high-throughput nanoliter dispensing liquid handling for micro-assays and macro arrays
• BioMek 2000 high-throughput robot liquid handing robot.
• Agilent BioAnalyzer 2100 for both RNA and DNA
• Agilent 2200 Tapestation Bioanalyzer for RNA and DNA
• Agilent hybridization chambers and incubators
• NanoDrop ND-1000 spectrophotometers and ND-3300 fluorospectrophotometer
• Molecular Devices/Axon four-laser confocal microarray scanner
• ICX-Nomadics SensiQ surface plasmon resonance instrument
• GeneMachine OmniGrid 100 environmentally-controlled pin-spotting system
• Tissue disruptors and bead-milling equipment
• SciGene Hybex Microarray system for multiplexed arrays and high-throughput hybridizations

Software (We work closely with the OSU High Performance Computing Center)

• Open Source: R-Package with BioConductor, Cluster, TreeView, Augustus, BioLinux, BioPerl, BLAST+, BRIG, Circos, ClonalFrame, Clustal_Omega, CONSED, PHRAP, Cufflinks, Cytoscape, Dendroscope, UGENE, PhyML, EMBOSS, JEMBOSS, Genome Workbench, Glimmer, Globus, Gnumeric, gPLINK, IGVTools, SAMtools, KEGG, MADAM, MAUVE, DReAMM, MEGAN, MEGA, Mothur, PLINK, Quast, Readseq, Newbler, SOAP, STRING, Trinity, Trinnotate, Velvet, and more.
• High Performance Computer Accounts: OSU Cowboy, OSU Cloud, OU Schooner, XSEDE, Cyverse (formerly iPlant), Galaxy, Shodor, and the Oklahoma Petastore.
• Commercial: GenePix v6 & v7

Training

• Workshops
• Individual consultations
• Data science curricula and curricula development