• Total RNA extraction (high throughput or column based)
• miRNA extraction
• PAXGene total RNA
• Assistance with Trizol extractions

• Genomic DNA extraction (high throughput or column based)
• HMW/UHMW long-DNA extraction for Long Read Sequencing (NEB Monarch)
• DNA extractions with bead beating (MagAttract/Kingfisher)

There are no sample minimums for extraction but please note flat rate labor charges will apply to select services from 1 – 192 samples.  Beyond 192 samples, a second flat rate charge will be added to the project.  Depending on sample number, most extraction services can be automated on the Kingfisher, however, a minimum of 48 samples or more may be required depending on the extraction kit.  

Nuclei extraction services are also available for plant and other tissues.  Singulator nuclei isolation or manual nuclei isolation available. Please inquire for pricing.

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