Equipment

Storage of biological samples

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

Sample processing, nucleic acid isolation, and quality control

• MP 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 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 of any magnetic particle-based kit to meet various application demands.

• NanoDrop 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. The 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.

• QIAxcel Advanced System: The QIAxcel Advanced system  provides high-throughput RNA and DNA analysis (up to 96 samples) using capillary based gel system. It allows for more efficient quality control of RNA and will serve as a replacement for standard agarose gel electrophoresis genotyping of PCR products. Thus, for most genotyping, the preparation of agarose gels, ethidium bromide staining, and image analysis will no longer need to be done. Additionally, the system can be configured to automatically call genotypes.   

• Perkin Elmer Zephyr G3 NGS Workstation: The Zephyr^® G3 NGS
  Workstation is a benchtop liquid handler designed to automate library preparation for next generation sequencing and address laboratory requirements for the physical separation of pre and post-PCR processes. The graphical user-interface and standardized deck with integrated hardware maximizes laboratory productivity while reducing variability resulting from manual pipetting steps. The workstation offers a walk away solution and flexible processing enabling the parallel processing of 8-96 NGS library or exome preparations or a 96-well plate of SPRI size selections / post-PCR clean-ups per run.

Medium throughput genetic/genomic analysis instrumentation

• Bio-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.

High-throughput genomic analysis using next-generation sequencing instrumentation

• Illumina iSeq100 platform: The Illumina iSeq100 platform is a desktop sequencer that very versatile sequencing from 1 X36 bp
  up to 2 X 150 paired-end reads in a single run ,generating  1.2 Gigabases (Gb) or up to 8 million sequencing reads in a single run.
  This can allow for performing amplicon sequencing, small genome sequencing and assembly, and enables detection of target variants
  with unmatched accuracy.
  
• Specifications

• Illumina MiSeq platform: The Illumina MiSeq platform is a desktopsequencer that can produce 2 x 300 paired-end reads in a single run
  and generated 15-20 Gigabases (Gb) or up to 50 million sequencing reads in a single run. This allows small genome sequencing and assembly, and enables detection of target variants with unmatched accuracy. In addition, this system is perfectly 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 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

• Illumina NextSeq2000 platform (New 2021): The IlluminaNextSeq200 is provides greater sequencing throughput compared to the NextSeq500,  including greater batching of human exomes, whole human genome, SARS-CoV2 genome sequencing, whole transcriptome analysis and single cell transcriptomics in a single run. The system is scalable and can run flow cells (P2) to generate similar amount of data compared to the NextSeq50, but more cost effectively as well as generate >300Gb or >2 billion reads in a single run using the P3 flow cells.
• Specifications

• 10X Chromium Single Cell Instrument: The 10X ChromiumInstrument enables the capture of individual biomedical material, such as DNA fragments or whole cells within tens of thousands of uniquely addressable partitions, each containing an identifying barcode for downstream analysis. The most important utility of this instrument is to perform single cell RNA sequencing (scRNAseq). scRNAseq has become an important research tool (both for basic science and clinically) allowing for simultaneous transcriptome analysis on individual cells/different cell types derived from complex tissues as opposed to performing sequencing on RNA isolated from an entire piece of tissue or even cell-culture studies. For example, an entire organ (e.g. kidney, brain, etc.) can be harvested, digested into a single cell suspension, and sequencing performed on 100- 80,000 individual cells. An added benefit of this technology is that it fully integrates with our current Illumina sequencing equipment, including the Illumina NextSeq 500 and 2000.

Preliminary bioinformatic tools and analysis

• DNAstar 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.

• Custom Bioinformatics via High Performance Computing: The Molecular and Genomics Core through its collaboration with MS-INBRE at University of Southern Mississippi has access to Magnolia Cluster/HPC as needed for the custom analysis of genomic data. This system provides:
  
  o   1896 compute cores
  
  o   7168 CUDA cores
  
  o   4 High memory nodes (512 GB RAM per node)
  
  o   20 cores, and 6 GB RAM per core on normal compute nodes
  
  o   Rapid temporary filesystem (LUSTRE) for application execution
  
  o   Network attached storage for data archiving