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Molecular and Genomics Core Facility

Equipment

The UMMC Molecular and Genomic Core Facility is located in G669 of the Guyton Building and occupies about 1,000 square feet of laboratory space. The core facility is well-equipped to perform genomic analysis in human and common model organisms. We are experienced in all aspects of molecular biology, including nucleic acid isolation, quality control, microarray, next-generation sequencing, gene-editing technologies, and bioinformatics.

Specific equipment housed in the core facility includes:

Storage of biological samples

  • Two -80ºC freezers, two -20ºC freezer and two 4°C refrigerators.

Sample processing, nucleic acid isolation, and quality control

  • MP Biomedic FastPace.jpgMP Biomedical FastPrep-96 instrument:
    This system is used to homogenize biological samples. It provides high-throughput processing (192 samples in 2 x 96 deep-well plates) of tissues and cells. The processed samples can then be used with KingFisher Flex instrument to quickly, easily and reproducibly isolate stable RNA, active proteins and full-length genomic DNA. 
  • kingfisher-flex-magnetic-particle-processor.jpgKingFisher Flex Magnetic Particle Processors - 96 and 24 Head:  
    The processor is for DNA/RNA, protein or cell purification from most sources. This system includes fully-automated high purification of nucleic acids, proteins and cells, This system can process up to 96 samples in under 20 minutes with additional flexibility that allows the use any of magnetic particle based kit to meet various application demands.
  • nanodrop-one-spectrophotometer.jpgNanoDrop ND-1000, NanoDrop One Microvolume UV-Vis Spectrophotometer, and Qubit Fluorimeter: These spectrophotometers allow micro-level quantitation of 1 µl of sample with high reproducibility. This allows sample measurement up to 50-fold higher in concentration than can be measured on classical 1 cm cuvette-based systems, virtually eliminating the need for dilutions. nanodrop-nd-1000-spectrophotometer.jpgThe NanoDrop One instrument provides more accurate determination of quantity and quality of DNA, RNA, and protein samples in seconds with 1-2 µl, including full-spectral data. This instrument offers more dynamic range (0.2-27,500 ng/µl dsDNA), greater wavelength range (190-850 nm), and higher spectral resolution. The Qubit Fluorimeter is a fluorescence-based system. DNA or RNA concentration is reported by a dye that emits a signal only when bound to the target, which minimizes the effects of contaminants such as degraded DNA or RNA.
  • bio-rad-experion-bioanalyzer.jpgTwo Bio-Rad Experion Bioanalyzers and one QIAxcel Advanced System: The bioanalyzer is used for nucleic acid and protein analysis using an integrated labchip system that performs multiple electrophoresis steps in up to 12 samples in one run. This instrument is used to assess nucleic acid quality for downstream genomic applications, in particular for quality control of RNA and RNA-derived libraries for next-generation sequencing.qiagen-qiaxcel-advanced-bioanalyzer.jpg The QIAxcel system provides high-throughput RNA and DNA analysis (up to 96 samples) using a capillary-based gel system. It allows for more efficient quality control of RNA and serves as a replacement for standard gel electrophoresis genotyping of PCR products. Thus, for most genotyping, the preparation of agarose gels, ethidium bromide staining and image analysis will no longer be needed. The system can also be configured to automatically call genotypes.  

Medium throughput genetic/genomic analysis instrumentation

  • bio-rad-cfx-384.jpgBio-Rad CFX96 and Bio-Rad CFX384 Real-Time PCR Detection Systems: These systems provide medium-throughput platform (n=1-384 samples) to perform gene expression/quantitative real-time PCR. These systems allow for quick set-up of runs and monitoring of amplification traces in real time on the integrated LCD touch screen. The CFX384 allows up to five-target detection and easy-to-use software to calculate fold-change between sample groups.
  • beckman-coulter-ceq8000xl-gexp-genetic-analysis-system.jpgBeckman CEQ 8000XL GeXP Genetic Analysis System: The system provides traditional Sanger sequencing (n=96 well-plate), genotyping, and gene expression capabilities.
  • affymetrix-genechip-scanner-3000-7g-system.jpgAffymetrix GeneChip Scanner 3000 7G System: This system provides a well-established, robust genomic analysis platform for human disease models (human, mouse, rat). The system also allows for genetic analysis in eukaryotic animal (Drosophila, zebrafish) and plant (rice, barley, cotton) systems, and prokaryotic organisms (E. coli). The system provides a diverse genomics platform, including differential expression levels, gene regulation (ChIP-chip, methylation), resequencing, quantification of copy number changes (CNV), and assessment of single nucleotide polymorphisms. While next-generation sequencing has become the preferred platform for gene expression, the Affymetrix system has significant utility for surveying SNP and CNV across the genome (CytoScan HD arrays).

High-throughput genomic analysis using next-generation sequencing instrumentation

  • illumina-miseq.jpgIllumina MiSeq platform: This MiSeq desktop sequencer can produce two 300 paired-end reads in one run and generate 15-20 Gigabases or up to 25 million sequencing reads in a single run. This allows small-genome sequencing and assembly and enables detection of target variants with unmatched accuracy. This system is suited to perform 16S microbial sequencing on up to 384 pooled samples, amplicon sequencing, and genotyping by sequencing of several hundred samples on a given run.\
  • Specifications
  • illumina-nextseq-500.jpgIllumina NextSeq500 platform: The platform delivers powerful high-throughput next generation sequencing with speed and simplicity. The fast, integrated, sample-to-results workflow enables many sequencing applications, including human exomes, whole human genome, and whole transcriptome analysis in a single run. The system can generate more than 120 GB or more than 800 million reads in one run.  The platform can be used in high- and mid-throughput sequencing applications.
  • Specifications
  • bio-rad-ddseq-single-cell-isolator.jpgBio-Rad ddSeq Single Cell Isolator: The isolator allows for transcriptome analysis of individual cells. The system uses Bio-Rad’s proprietary technology to capture individual cells within a small droplet. Each individual cell, in combination with specialized Illumina Library Prep and integration with our existing equipment (Illumina MiSeq or NextSeq500), will generate single cell transcriptome profiles (on 4 groups of 300-400 cells or 1 group of 1,500 cells). This technology allows for an evaluation of individual cell transcriptomes, thus providing a high-resolution view of cell-to-cell variation.

Preliminary bioinformatic tools and analysis

  • bioinformatics-analysis.jpgDNAstar Suite sequence analysis tools:  
    These tools provide the software for next-generation sequence assembly and analysis. They support all major NGS technologies, allowing easy use of genomic data for de novo or reference-guided genome assemblies, targeted resequencing, metagenome and population assemblies, large-scale multi-sample SNP analysis, RNAseq, ChIPseq, and miRNA alignment and analysis. A network license that runs on genomics core servers allows for three concurrent users. The software client can be installed on any genomics core user’s computer providing access to a variety of genome analysis tools.
  • Onsite and Cloud Illumina BaseSpace platform: The BaseSpace Sequence Hub offers a variety of NGS data analysis applications that are developed or optimized by Illumina, as well as growing selection of third-party app providers. In total, these apps cover all the common analysis methods used with Illumina NGS data, including RNAseq, exome/enrichment, amplicon, whole-genome sequencing, de novo assembly, and 16S metagenomics data analysis. A complete list of analysis tools can be found by clicking here. The Molecular and Genomics Core currently has an Onsite BaseSpace server that provides analysis tools behind our UMMC firewall and within our network. In addition, the core also has a professional subscription to Cloud BaseSpace Hub, which provides the core and its clients access to high-speed computing capabilities for large scale projects.
  • Qiagen Ingenuity Pathway Analysis: The IPA allows the user to model, analyze, and understand the complex biological and chemical systems at the core of life science research. This software includes capabilities for pathway analysis, predictive casual analytics and NGS/RNAseq data analysis.