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Summary of Genomics Services

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.


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

 

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