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Biosample Laboratory Services

Nucleic Acid Services

Nucleic Acidservices

Nucleic acid processing and extraction services are offered for whole blood, biofluids and tissue. We offer flexible DNA extraction capabilities consisting of organic, solid-phase, salting out and bead-based extractions chemistries from virtually any tissue source. We process and extract RNA collected and stored from frozen tissue biopsies, FFPE block/slides, Paxgene RNA tubes, PaxTissue containers, RNAlater and Genotek Oragene RNA collection tubes. We have extensive experience in protocol development and can provide expertise to ensure the right technique is applied for each requisite tissue/sample type.

DNA Extraction

RUCDR Infinite Biologics uses all methods for DNA extraction including salting out, magnetic beads, solid phase and organic phase. All of these methods can be automated with the exception of the organic method.


  • Salting Out
      Autopure
    • Autopure (Qiagen) - The Autopure LS uses Puregene chemistry to enable automated purification of genomic DNA from large-volume samples from a broad range of sample types. Purified DNA generated from the Autopure is highly stable and routinely yields up to 350 ug of DNA per 10 ml of blood.
  • Magnetic Bead
    • Hamilton Chemagic Star - uses a magnetic bead technology to extract nucleic acids from a wide range of human sample materials (Blood, plasma, Buffy coat, saliva, cells, tissue, buccal swabs). This robust instrumentation can extract nucleic acids from sets of samples with volumes ranging from 20 ul to 10 ml in 2.5 to 4 hours.
    • Qiagen EZ1 - The Qiagen BioRobot EZ1 is a magnetic bead-based nucleic acid extractor capable of purifying DNA from whole blood, cultured cells, buffy coat, buccal swabs, dried blood spot cards, bacteria, viruses, tissue, FFPE and forensic samples. The EZ1 can process up to 6 samples in 25 minutes. The starting material is lysed and the DNA is bound to magnetic beads. The magnetic beads are transferred from one reagent to the next and after a series of washes, the nucleic acids are eluted into a special elution buffer. The nucleic acids can be used directly in downstream assays without further processing.
    • QIA symphony Sample Prep
    • Qiagen QIAsymphony - The QIAsymphony Sample Prep by Qiagen is a fully automated nucleic acid extractor and liquid handler capable of purifying DNA from whole blood, cultured cells, buffy coat, tissue, FFPE, plasma/serum and bacterial cultures. The biomaterial is lysed and/or mechanically disrupted, releasing the nucleic acids into the solution. Binding buffer is added to precipitate nucleic acids, which then bind to the magnetic beads. The magnetic beads are collected with a magnet and washed several times. At the end of the procedure, the nucleic acids are eluted from the beads with a special buffer. The QIAsymphony can process up to 96 samples within 6.5 hours.
    • Agencourt DNAdvance - The Agencourt DNAdvance is a magnetic bead-based extraction technology that can isolate human DNA from cells and tissues. The DNAdvance has been customized to work with the Beckman Biomek FX automated liquid handler to create a high-throughput DNA extractor specialized for small quantities of cells and tissues.
  • Solid Phase
    • Qiagen BioRobot Universal - The Qiagen BioRobot Universal is a fully automated nucleic acid extractor capable of isolating DNA from whole blood, buccal swabs and forensic samples. The Universal relies on a unique solid-phase extraction technology that utilizes a filter plate to trap and isolate nucleic acids. DNA is isolated, washed and eluted into a storage buffer. The Universal can process up to 192 samples in 5.5 hours.
  • Organic Phase Organic phase extraction
    • Phenol Chloroform - Organic phase extraction remains the gold standard in DNA purification techniques. After lysis, phenol-chloroform is used to separate nucleic acids from proteins and lipids. Precipitation and washing with alcohol results in pure DNA that is resuspended in a storage buffer. Phenol-chloroform DNA extraction is used primarily for old or compromised samples which require special processing.

RNA Extraction

RNA is extracted using automated solid phase extraction and bead based chemistries, which allows for the isolation/enrichment of micro RNA species (miRNA) in an aliquot separate from the total RNA, within the same workflow. Following extraction, samples are transferred directly into 2D-barcoded tubes and a 2 ul sample for QC is immediately removed by Hamilton STAR automation for analytical and, in some instances, functional QC.


  • Magnetic Bead
      Chemagic Star
    • Chemagic Star - Manual extraction of RNA is labor intensive and introduces the potential for human error. The Chemagic STAR reduces the risk of error and ensures higher sample quality by: eliminating manual pipetting steps; reducing the risk of cross-contamination; providing faster assay setup; and ensuring consistency of sample processing by removing user variability. The Chemagic STAR utilizes a unique paramagnetic bead technology to purify RNA from PAXgene™ blood. After sample lysis, total RNA is precipitated and bound to the beads. A magnet is used to isolate the beads from solution and wash the RNA before eluting into a special buffer. The Chemagic STAR RNA method isolates total RNA, including smaller types such as miRNA.
  • Solid Phase
    • Qiagen Universal - The Qiagen BioRobot Universal is a fully automated nucleic acid extractor capable of isolating RNA from PAXgene blood, cultured cell pellets and tissues. The Universal relies on a unique solid-phase extraction technology that utilizes a filter plate to trap and isolate nucleic acids. Total RNA is isolated, washed and eluted into a storage buffer. A secondary protocol is available for the enrichment of miRNA, which normally can be difficult to isolate. The Universal can process up to 192 samples in 5.5 hours.
  • Organic Phase
    • Phenol Chloroform - Organic phase extraction results in high purity RNA. After lysis, phenol-chloroform is used to separate nucleic acids from proteins and lipids. Precipitation and washing with alcohol results in pure RNA that is resuspended in a storage buffer. Phenol-chloroform RNA extraction is used primarily for old or compromised samples which require special processing.

Nucleic Acid Quality Control

After extraction, all nucleic acid samples are subject to comprehensive analytical and functional quality control procedures. Analytical quality control consists of concentration, purity and volume measurements utilizing cuvetteless spectroscopy that measures contaminant profiles allowing for precision measurement of nucleic acid. Functional quality control consists of the RUID quality panel for DNA. Our quality control provision is state of the art and in place to ensure sample quality and integrity for downstream analysis.


  • Analytical Quality Control
    • VolumeCheck - The VolumeCheck uses ultrasonic technology to measure height of the sample meniscus. This is all performed without contacting the sample.
    • Trinean96
    • Trinean DropSense96 - Concentration is measured using the Trinean DropSense96. The DropSense96 is a multichannel spectrophotometer that uses UV/VIS spectral analysis to quantify microliter droplets of DNA or RNA. Data generated from the DropSense 96 is highly robust and measure contaminates, as well as double stranded DNA as low as 5 ng/ul.
  • Functional Quality Control
    • Caliper LabChipGX - Each RNA sample is analyzed to measure RNA integrity (analyzing the intactness of ribosomal subunits in total RNA). The LabChipGX allows for the measurement of 96 or 384 samples in a single run. A RQS score is calculated for each total RNA and stored as part of the QC workflow. Total RNA from whole blood is functionally assessed using a proprietary RUIDGx™ fidelity measurement panel.
    • SNP prototyping using RUID
    • RUID™ - SNP Genotyping is performed via RUCDR Infinite Biologic’s proprietary RUID panel. A panel of 96 SNPs was developed as the main functional component of this quality control schema. SNPs were selected based on criteria that include representation of the genome, markers in polymorphic regions to confer unique identity to each sample, selection of ancestry markers to determine ethnicity, and selection of SNPs represented on commercial array based platforms to use as verification markers for GWAS. This patent pending technology allows for immediate reconciliation of sample collection and registration errors in addition to qualifying each and every DNA prior to costly downstream analyses.
    • RUIDGX™ - RNA is quality controlled using the RUIDGx™ quality panel. This approach analyzes tissue-specific transcripts that interrogate the entire length of selected transcripts as well as a variety of expression levels. This rapid analysis provides direct assessment of cDNA fidelity and provides a score for each sample which correlates directly with microarray and RNAseq performance for any sample.

Nucleic Acid Amplification

RUCDR offers multiple solutions for the robust amplification of precious nucleic acid samples, as well as restoration of degraded or compromised material. Nanogram quantities of starting material are converted into microgram quantities for storage or downstream applications. Whole-genome and whole-transcriptome amplification chemistries enable highly uniform and unbiased enrichment, preserving relative abundance and allelic balance for downstream genetic analyses. Amplified template is suitable for qPCR, microarray and Next-Generation Sequencing applications.


  • Qiagen REPLI-g Midi Kit – Yields of up to 40ug of high molecular weight DNA, >10 kb in length
  • Qiagen REPLI-g FFPE Kit– Yields of up to 40ug of DNA from FFPE tissue sections. Degraded fragments are randomly concatamerized to form a suitable substrate for amplification, producing amplified material that is suitable for hybridization-based assays.
  • NuGEN whole-genome and whole-transcriptome amplification kits – NuGEN SPIA (Single Primer Isothermal Amplification) technology is a sensitive, high-fidelity amplification method that enables global genomic analysis of amplified product. NuGEN amplification is integrated into qPCR, microarray and Next-Generation Sequencing services.
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145 Bevier Road Piscataway NJ 08854-8009
p 732 445 1498 f 732 445 1149 www.rucdr.org