Our sptlabtech firefly+ is a liquid handler with an integrated thermocycler and labware capability specifically designed for high throughput NGS library preparation.

The Opentron OT-2 liquid handlers are capable of single and 8 channel pipetting from 0.1ul-100ul.

The CGI instrument will soon be replaced by the Firefly+, which offers higher accuracy, the ability to design protocols on instrument, and the addition of cooling stacks and an integrated PCR machine.

The QIAcube is an automated sample preparation instrument designed to streamline DNA, RNA and protein spin column purifications. The system processes up to 12 samples per run and integrates a centrifuge, heated shaker, pipetting system, and robotic gripper.

The QIAgility is a compact benchtop instrument that automates PCR and qPCR setup (tube and plate formats) to improve lab productivity and reduce human error.

The Agilent 4200 TapeStation is an automated electrophoresis platform used as a critical QC checkpoint at multiple stages of the next-generation sequencing (NGS) workflow, helping labs avoid wasted sequencing runs on poor-quality libraries or degraded input material.

Role in the NGS workflow:

1. Input sample QC (pre-library prep) 
   • Assesses genomic DNA integrity (DIN score) to flag degraded samples before they enter costly library prep
   • Evaluates RNA quality (RIN score) for RNA-seq applications, ensuring sufficient integrity for reliable transcript representation
2. Library QC (post-library prep) 
   • Confirms successful adapter ligation and fragment size distribution
   • Detects adapter dimers, primer dimers, or incomplete size selection—common failure points in library prep
   • Verifies library size matches expected insert size for the sequencing chemistry (e.g., Illumina, PacBio)
3. Pooling/normalization support 
   • Provides molarity estimates (combined with fragment size) to enable accurate library pooling ratios
   • Ensures balanced representation across multiplexed samples, critical for even read depth across a flow cell

Why it matters for NGS specifically:

• Prevents flow cell failures: Catching poor libraries before loading avoids wasting expensive sequencing reagents and run time
• High-throughput compatible: 96-sample ScreenTape format matches typical NGS batch sizes
• Fast turnaround: ~1 minute per sample keeps pace with prep timelines without becoming a bottleneck
• Reproducibility: Automated handling reduces operator-to-operator variability compared to manual gel-based sizing (important when running standardized clinical or CLIA-compliant pipelines)

Common ScreenTape assays used in NGS labs:

• Genomic DNA ScreenTape (input QC)
• RNA ScreenTape / High Sensitivity RNA ScreenTape (RNA-seq input)
• D1000/D5000 or High Sensitivity D1000/D5000 ScreenTape (library sizing)
• Cell-free DNA ScreenTape (liquid biopsy/cfDNA-based NGS)

The Agilent Femto Pulse is an automated capillary electrophoresis (CE) system designed for high-sensitivity sizing and quality assessment of nucleic acids, with particular strength in analyzing large DNA fragments (up to ~165 kb) and detecting trace-level degradation that other platforms may miss.

Key features:

• Capillary electrophoresis technology: Uses a 12- capillary array format for automated, parallel sample separation—no gels or ScreenTapes required
• Ultra-high sensitivity: Detects DNA/RNA concentrations as low as ~0.5 pg/µL, ideal for precious or limited samples
• Wide dynamic range: Accurately sizes fragments from very small (short RNA/small RNA) to very large (>165 kb genomic DNA)
• Automation: Minimal hands-on time; automated injection, separation, and detection
• Throughput: Processes up to 96 samples per run depending on capillary array configuration
• Software: Agilent ProSize software generates electropherograms, gel-like images, sizing tables, and quality scores (e.g., Genomic Quality Number, GQN)

Primary applications:

• High molecular weight (HMW) gDNA QC: Critical for long-read sequencing platforms (PacBio, Oxford Nanopore) where input DNA integrity directly impacts read length
• Genome quality scoring (GQN): Quantifies the proportion of DNA above a user-defined size threshold, giving a more precise integrity metric than traditional gel electrophoresis
• Plasmid and AAV/viral vector analysis: Sizing and purity checks for gene therapy and vector-based workflows
• NGS library QC: Particularly for long-read library prep, where accurate large-fragment sizing is essential

Why it’s used:
The Femto Pulse fills a gap left by traditional gel electrophoresis and lower-sensitivity CE systems (like the TapeStation) — namely, precise characterization of high molecular weight and ultra-low concentration samples. This makes it especially valuable in long-read sequencing, gene therapy/viral vector production, and any application where fragment size and integrity at the high end of the scale are critical to downstream success.

Common assay kits:

• Genomic DNA 165 kb Kit (HMW DNA analysis)
• gDNA/AAV/Plasmid analysis kits (vector-based workflows)

The Qubit Fluorometer is a standard companion instrument alongside the TapeStation/Femto Pulse (for sizing/integrity) —TapeStation/Femto Pulse assess fragment size and quality, while Qubit provides highly accurate, fluorescence-based quantification of DNA, RNA, and protein concentrations in a sample as well as the precise concentration measurement needed for accurate library pooling and sequencer loading .

• NGS library quantification: Accurate measurement of final library concentration before pooling and loading onto a sequencer—critical since qPCR or fluorometric quantification (not absorbance) is the gold standard for NGS
• gDNA/RNA input QC: Confirms concentration of extracted nucleic acids before library prep or other downstream applications
• Low-concentration samples: High Sensitivity (HS) assay kits detect concentrations as low as ~0.2 ng/µL, useful for precious or limited samples

Common assay kits:

• Qubit dsDNA HS (High Sensitivity) and BR (Broad Range) Assay Kits
• Qubit RNA HS and BR Assay Kits
• Qubit ssDNA Assay Kit

• Thermo-Fisher NanoDrop 2000
• Agarose gel electrophoresis systems

The MP Biomedical FastPrep 24 System is a high-speed beat beating system capable of lysing/homogenizing up to 24 samples.

The Qiagen TissueLyser is a high-throughput bead mill homogenizer designed for parallel disruption of biological samples in tubes or 96-well formats. Developed jointly with Retsch, this original TissueLyser model processes up to 192 samples per run with adjustable frequency control from 3–30 Hz and timed runs from seconds to nearly 100 minutes, giving labs tight control over energy input for DNA, RNA, and protein workflows.

Sage Science’s Pippin systems use disposable gel cassettes with each lane physically separated from others to eliminate cross -contamination. DNA sizing is determined by the detection of markers in a dedicated lane or internally in the sample lane and using those to select and collect the desired fragments based on user-input values.

Pippin Prep: fragments from 100 bp to 1.5 kb

PippinHT: fragments from 100 bp to 1.5 kb for up to 24 samples.

Blue Pippen: pulse field version with a fragment range of 100 bp to 50Kb.

The HLS system can extract HMW DNA from cells and size fractionate/collect DNA fragments up to 2MB.

The HLS system also supports CRISPR-CATCH. CRISPR/Cas9 can be used to design targeted purification of large genomic regions or genes. This in vitro application with Cas9, termed CATCH, can enhance study of structural variation and provide valuable phasing information. Casettes process cell samples from extraction, through Cas9 Targeting (regions up to 1MB) and enrichment of size selected DNA.

The Covaris M220 is a compact focused-sonicator (75W) for DNA shearing.

The Covaris S220 is a focused-ultrasonicator (100W) is a high power system engineered for pre-analytical sample processing using Covaris’ patented Adaptive Focused Acoustics^® (AFA^®). Utilizing a spherical acoustic transducer, specifically designed acoustical cuvettes and advanced electronics, AFA delivers controlled energy precisely and accurately to sample volumes from 15 μl to 130ul. This instrument offers continuous temperature control using an integrated chiller.

Through a collaborating lab in the Engineering and Science Building, the CGI has access to the CP02 cryoPREP^® Automated Dry Pulverizer. This instrument uses a calibrated and controlled mechanical force to cryofracture flash-frozen tissues within a mass range of 15 mg to 2 g. The dry pulverization process disrupts the extra-cellular tissue matrix and increases the tissue surface area, thus improving the extraction efficiency of biomolecules, while minimizing sample loss during the process. The increased surface area reduces the distance a stabilizing extraction buffer need to diffuse during subsequent lysis steps.

The Hologic Diagenode Megaruptor 3 is available through a collaborating laboratory in the Engineering and Science Building. The Megaruptor 3 uses single sample cassettes to shear DNA for optimal long-read sequencing using PacBio and Oxford Nanopore Technologies. This instrument can shear 1-8 samples in parallel and shear DNA to a target size within the range of 5 kb-100 kb.

ThermoFisher’s KingFisher instruments are bench top purification instruments that use permanent magnetic rods with disposable tip combs to collect beads from solution, then release them into successive wells, each containing reagents for the next step of isolation. This highly effective method of bead collection and transfer leads to clean extractions, efficient results, and preservation of sample. Using a simple process (bind, wash, elute), KingFisher instruments can automate the extraction of any analyte of interest that can be bound to a bead, even from challenging samples.

The CGI has a Kingfisher Apex, capable of extracting 24 or 96 samples per run and implements UV decontamination between runs.

The Singulator S200+ from S2 Genomics is an automated system that dissociates fresh, frozen or archival FFPE tissue samples into single-cell or nuclei suspensions.

FFPE Automated Processing: Handles deparaffinization, rehydration, and nuclei isolation from archival blocks with minimal manual steps.
Low Sample Input: Works with inputs as low as 2 mg of tissue or a 50 µm curl. 
Speed & Control: Completes automated FFPE nuclei extraction in roughly 60 minutes. Completes fresh tissue dissociation in minutes using a dual-cartridge system. 
Downstream Compatibility: Prepares samples for single-cell/nuclear RNA sequencing (scRNA-Seq, snRNA-Seq), ATAC-Seq, and spatial transcriptomics.