dsDNA Core Equipment & Services
King Fisher Duo Prime
The King Fisher Duo Prime system isolates DNA, RNA, and proteins from a variety of starting materials including cell-free body fluids, blood, bacteria, cell cultures, tissue and plant samples. The automated magnetic bead technology allows excellent recovery of samples with great reproducibility and efficiency.
QiaCube Connect MDx
The QIAcube Connect MDx is suitable for academic as well as pharmaceutical, biotechnology, and biomedical research. The system offers over 150 standard protocols, including several IVD protocols to perform automated DNA, RNA, and protein sample processing for a large range of research and clinical sample types. This can be seamlessly integrated with down-stream assays including NGS, genotyping, gene expression analysis, and microbiome research.
Invitrogen Qubit
Qubit fluorometers detect fluorescent dyes that are specific to the sample type (DNA, RNA, and protein). The Qubit assay selectively detects DNA, RNA, and protein using UV absorbance. The assay requires only a small amount (1 μL) of sample and detects as little as 10 pg/μL of DNA. Qubit nucleic acid quantification is considered the gold standard for downstream applications such as NGS.
Agilent Bioanalyzer
High-quality starting material is crucial for efficient NGS analysis. The Agilent 2100 Bio-analyzer system effectively determines RNA and DNA sample quality. It is suitable for sample NGS quality control (size distribution analyses and QC of amplified DNA libraries), PCR validation and impurity check, restriction digestion analysis, and genotyping analysis.
Femto Pulse System
Quantify, qualify, and size DNA and RNA samples with accuracy and precision
The Femto Pulse system provides researchers with a powerful and automated pulsed-field capillary electrophoresis system. Easily achieve 10 times higher sensitivity for smears and up to 100 times for fragments. A meticulously designed optical detection platform and pulsed-field power enable unprecedented sensitivity, detecting nucleic acids into the lower femtogram range. With the ability to separate DNA and RNA samples, the Femto Pulse system is flexible enough to handle any of your workflow scenarios.
BluePippin
The BluePippin has the DNA size selection capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size thresh-old set by the user. The cassettes for DNA selections are available in four concentrations to provide a full range of size selection options between 100 bp and 50 kb.
Covaris Focused-Ultrasonicator
The generation of DNA fragments in epigenomics study is a critical sample preparation step required by all NGS library constructions. Covaris adaptive focused acoustics (AFA) transmits acoustic energy isothermally to ensure both unbiased fragmentation and high recovery of double-stranded DNA. The M220 focused-ultrasonicator generates fragment lengths from 150 bp to 1.5 kb in a micro-TUBE, and to 2, 3, and 5 kb in a miniTUBE. This technology performs standardized frag-mentation regardless of GC/AT percentage.
Eppendorf epMotion
The epMotion is an automated liquid handler system specifically for genomics applications. The system uses a powerful Magnum FLX magnet for bead-based purification in plates with minimal elution volumes. With high pipetting accuracy and precision, the epMotion 5075tc increases productivity and provides rapid and reproducible results.
Opentrons Flex NGS Robot
For scaling up and fully automating end-to-end NGS library prep.
With the Flex NGS Workstation, you can automate your NGS workflow at the scale you need to increase efficiency, reduce errors, and save hands-on time. The Flex enables you to automate your library prep and pre-sequencing workflows using any leading reagent system on the market, including fragmentation and tagmentation protocols.
Opentrons OT-2 Robot
The Opentrons® OT-2 is a high-precision, open-source liquid handler designed to be easy for scientists to use and flexible enough to automate many application workflows. This robot and its accompanying automation platform are used to automate hundreds of protocols and workflows in genomics, proteomics, cell-based assays, and drug discovery.
Illumina MiSeq
The MiSeq System facilitates research with a wide range of sequencing applications. It is capable of automated paired-end reads up to 600 bp and produces up to 15 Gb per run. With the longest read length of any Illumina platform, it can produce up to 25 million sequencing reads. The library prep kits it uses are optimized for a variety of applications, including targeted gene sequencing, small genome sequencing, metagenomics, and plasmid sequencing.
PacBio Sequel IIe
The Sequel IIe system is a third-generation sequencer that performs highly accurate “HiFi” long-read sequencing. For de novo genome HiFi sequencing on the Sequel IIe, each SMRTcell can generate up to 35Gb HiFi data with a 15-20kb insert size. Using SMRT sequencing technology, its applications include iso-seq, epigenetics, whole genome sequencing (humans, plants, animals, and microbes), targeted sequencing, and complex population sequencing.
Illumina NextSeq 2000 Sequencing Systems
The NextSeq 2000 System offers innovative design features, advanced chemistry, simplified bioinformatics, and an intuitive workflow that enable the widest range of applications and flexibility of scale on a benchtop sequencing system.
Illumina MiSeq i100 Plus
The MiSeq i100 and MiSeq i100 Plus Systems provide results 4× faster than the MiSeq System, with sequencing run times as fast as four hours.
With the expanded output offered by the MiSeq i100 Series, you can increase sample throughput, perform deeper sequencing, and gain more insights for a wide range of applications faster than ever. XLEAP-SBS chemistry on the MiSeq i100 Series eliminates thawing requirements so reagents can be used whenever your sample is ready.
SeqStudio Flex genetic analyzers
Flexibility, usability, connectivity, and serviceability in a mid-throughput genetic analyzer
The Applied Biosystems SeqStudio Flex Series genetic analyzers deliver the high level of Sanger sequencing and fragment analysis data quality and reliable performance that scientists need, while leveraging design improvements and technological advances for increased flexibility, easier operation, enhanced connectivity, and remote serviceability.
With a wide range of applications from simple, targeted sequencing to identification of the latest SARS variant of concern, SeqStudio Flex genetic analyzers help you to achieve freedom and peace of mind, providing extra time in your day to do what you do best: answering the big scientific questions.
Bioinformatics Services
- Genomics & NGS Analysis – Quality control, assembly, annotation, variant calling, and comparative genomics for bacterial, plant, and animal datasets
- Metagenomics & Microbiome Profiling – Community composition, functional annotation, and gene tracking
- Transcriptomics & Gene Expression – RNA-seq preprocessing, normalization, differential expression, pathway enrichment, and visualization
- Phylogenetics & Evolutionary Analysis – Multiple sequence alignment, tree building, molecular evolution tests, and visualization
- Custom Bioinformatics Pipelines – End-to-end reproducible workflows for genomics, transcriptomics, and multi-omics, built with scalability, transparency, and fair data principles
Data Analysis Services
- Machine Learning & AI - Supervised/unsupervised modeling, deep learning, model selection and evaluation, error analysis, and deployment-ready inference
- Computer Vision & Image Analytics - Detection, segmentation, morphometrics, and batch inference pipelines for microscopy, biomedical, remote sensing, and other large image sets
- Natural Language & Text Mining - Corpus cleaning, topic modeling, document classification, and information extraction with transparent, reproducible workflows
- Time-Series & Forecasting - Signal preprocessing, feature engineering, forecasting, anomaly/change-point detection, and backtesting
- Network/Graph Analytics - Graph construction, embeddings, community detection, and path/flow analysis for interaction, connectome-like, and systems data
- Statistical Modeling & Inference - Study design support; GLMs/mixed-effects; nonparametric and resampling methods; diagnostics; publication-grade tables/figures
- Custom Pipelines & Automation - End-to-end data pipelines (ingest → clean → analyze → report), containerized or Slurm-scheduled; unit-tested, documented, and version-controlled
- Reproducible Reporting & Visualization - Notebook-driven analyses (Jupyter/R Markdown), figure suites, and optional dashboards with one-click rebuilds
- Data Management & FAIR Readiness - Project scaffolds, metadata, provenance, storage/archival plans, and handoffs that keep research organized and reusable
- Full-Service Analysis - We perform the analysis and deliver a report, figures, code, and rerunnable workflows
- Managed Compute Runs - You provide scripts/containers; we schedule, monitor, and return outputs/logs
- Self-Service HPC - You log in and run your own jobs with our templates and best-practice guidance
HPC Cluster
Platform: Hyper-Hornet (High-Performance Computing)
- CPUs: 2 × AMD EPYC 9654 (192 total cores)
- GPUs: 8 × NVIDIA H100 (80 GB, PCIe) with NVLink bridge interconnects
- Memory: 1.5 TB DDR5
- NVMe Storage: ~78.7 TB total (scratch: 61.44 TB; project: 15.36 TB; OS: 1.92 TB)
- OS/Frameworks: Ubuntu 22.04 with the Lambda Stack (CUDA/cuDNN, PyTorch, TensorFlow, and related ML frameworks)
- Access & Tooling: JupyterHub, RStudio Server, and secure remote desktops for GUI tools; Slurm scheduling with CPU/GPU profiles; languages/environments include Python, R, Julia, Rust, and Octave
- Networking: Dual 10 GbE (with out-of-band IPMI for management)
What You Receive
- Clear deliverables matched to your request (e.g., trained models, curated datasets, aligned/processed tables, validated figures, and a concise written report)
- Reproducible assets (code, notebooks, environment files, and Slurm templates) so results can be verified and extended
- Practical guidance for next steps (e.g., deployment options, scaling plans, or follow-on analyses)
Example Use Cases
- Image-heavy projects (microscopy, satellite/agricultural, clinical imaging) that need robust detection/segmentation at scale
- Multi-omics and large-table modeling (feature engineering, classification/regression, variable selection, and interpretability)
- Time-series forecasting and anomaly detection for sensors, experiments, or operational data
- Text mining for literature, reports, or survey free-text with transparent, auditable pipelines
- Team science projects that need maintainable, automated pipelines and reproducible reporting
Getting Started: Request a consultation or service through the Core’s request portal (iLab or campus service form)
Bio-Rad Next Generation Chromatography (NGC) System
The NGC Quest Plus system provides accurate gradients for high-resolution separations for any biological molecules. The system is equipped with a multi-wavelength detector with simultaneous four-wavelength monitoring (between 190 and 800 nm) for high-accuracy detection of proteins and peptides combined with conductivity measurements. Fractionated samples can be easily collected from analytical- to preparative-scale purifications using the fraction collector.
Applied Biosystems StepOne Plus Real-time PCR System
The StepOne Plus Real-time PCR System is a thermal cycler that uses robust LED based multiplex-color (FAM/SYBR Green, VIC/JOE, NED/TAMRA, and ROX) optical recording to deliver precise, quantitative real-time amplification results for a variety of genomic research applications including SNP genotyping, gene expression analysis, microRNA expression, protein expression, translocation analysis, gene detection, and viral load analysis.
We also offer a variety of non-NGS based services including:
- Recombinant protein production in yeast and E. coli. expression system
- Protein/enzyme purification
- Sub-cloning
- Bacterial identification
- Biochemical analysis