The Center for Genes, Environment and Health has established the Genetics Core Services at National Jewish Health. The core makes available to the research community (numerous or several) basic technologies which are of widespread general interest to those involved in genetics or molecular biology programs. The Center is able to provide these services with all necessary expertise and technical support at a reasonable cost.

Contact Information

Mailing Address:
Center for Genes, Environment and Health
c\o Ayndrea Greenfield
Smith Building; A642
1400 Jackson Street
Denver, CO 80206

PH: 303.270.2769
FAX: 303.270.2136


Equipment and Technologies


The Agilent microarray scanner is a versatile instrument used for all microarray applications, including gene expression profiling, high-density comparative genomic hybridization (CGH), and DNA methylation. Services: Standard core services currently include gene expression profiling using the Single Color, Quick Amp and Low Input Quick Amp labeling kits on the Agilent 4x44K microarrays. Other formats available and priced upon request. Total RNA samples should contain 10 to 200 ng in a volume of 1.5 µl. A quality assessment of RNA integrity should be made on the Agilent 2100 Bioanalyzer. Samples should have a RIN value of at least 7 before proceeding.
The high-resolution (2 um) of the MS 200 scanner from Nimblegen combined with the 12-bay MAUI Hybridization station make this a powerful platform for Gene Expression, Comparative Genomic Hybridization (CGH) studies, DNA Methylation, and analysis of ChIP-chip arrays.
The Tecan Freedom EVO is an extremely powerful instrument for the automation of liquid handling operations to provide accurate, high-throughput processing with minimal hands-on requirement. The robot is equipped with 8 fixed tips, plate manipulator arm (ROMA), tube barcode reader, and Infinite 200 plate reader. It is ideal for all repetitive operations including, dilutions and plating, cherry picking (hit picking), normalizations, Pico-Green measurements, reaction setup, and sequencing reaction cleanup. Fully programmable, the Tecan Freedom EVO can be configured to meet virtually any liquid handling needs.
Automated DNA/RNA purification from a variety of sample sources is being accomplished with a Qiagen BioRobot Universal system. All Qiagen 96-well format kits (DNAEasy, RNAEasy, PAXGene blood DNA etc.) can be automated on this robot to achieve high-quality DNA/RNA extractions and consistent results. BioRobot Universal is also used to perform numerous liquid handling tasks including sample normalization, PCR reaction setup, PCR clean up.
The Autopure LS enables automated purification of genomic DNA from large-volume samples using proven Puregene® chemistry. Manual handling of potentially-infectious samples is minimized. High-quality, purified DNA is stable for long-term storage and suitable for archiving as well as any downstream application. For increased convenience and flexibility, samples can be processed in batches of 8 or 16. Easy-to-use Autopure software provides diagnostic and troubleshooting functions that enable users to view the state of the instrument. To simplify data collection, information from each run is automatically stored in an integrated, searchable database.
Considered to be the “gold standard” in real time PCR, the 7900 from Applied Biosystems combines the flexibility in PCR chemistry with 96 or 384 well capacity.
The OpenArray system provides an efficient and cost-effective platform to perform high-throughput, real-time PCR assays. On a chip the size of a standard microscope slide, 3072 individual PCR reactions may be performed simultaneously using either Taq-Man, or SYBR chemistry. The high-density format eliminates the need for multiplexing so that performance may be optimized. The Accufill loading system takes only minutes to run and assures that samples are handled without fear of contamination. The system is ideal for gene expression and genotyping studies. Numerous pre-configured panels are available from Applied Biosystems (Click here) or researchers may create panels which are completely customized. For absolute quantitation of message transcripts, the OpenArray platform is perfect for running digital PCR experiments.
The BeadXpress reader by Illumina is ideally suited for medium-throughput, targeted genotyping projects, allowing 48, 96 or 384 multiplexed SNP assays using GoldenGate chemistry on Veracode beads with samples in the 96-well plate format. The Genetics Core can assist with assay design and submission to Illumina for assay production. GoldenGate genotyping generally requires two days of laboratory processing time. DNA should be submitted at a concentration of no less than 50 ng/ul.
The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA and RNA on a single platform. Results are delivered within 30-40 minutes in automated, high quality digital data. The Lab-on-a-chip platform is easy to use, faster than gels, and highly reproducible. The Bioanalyzer is also invaluable for making quality assessments at critical steps in the preparation of samples for microarray analysis.
Capillary DNA sequencing at the Genetics Core is carried out on an Applied Biosystems, 96-capillary, 3730xl DNA analyzer, which is the most advanced capillary sequencing platform available today. High quality reads in excess of 800 nt can be routinely achieved with proper sample preparation.

Multiple levels of service are available to meet the needs of the National Jewish Health and University of Colorado Denver research community. Those preferring to run their own Big Dye reactions (versions 1.1 or 3.1) can submit them to the core in a dried, “instrument Ready” form. Alternatively, primer and template may be submitted in the proper volumes and concentrations. The core will perform cycle sequencing, reaction clean-up, and provide data in a timely manner. Typically BigDye Terminator v3.1 cycle sequencing chemistry is used unless other chemistries are requested. Data for instrument ready samples are available by 10:00 am the following business morning. Full service samples submitted by 10:00 am will also processed within 24 hours.
The 5500xl Series Genetic Analysis System is a highly accurate, massively parallel next generation sequencing platform that supports a wide range of applications. The instrument is capable of sequencing 100Gb of mappable data, with reads length of 75bp. Reads can be multiplexed using 96 barcodes for DNA applications and 48 barcodes for sequencing RNA applications. The flexibility of independently run lanes in the microfluidic flowchip and multiplexing capability allow you to run a single lane quickly or conduct multiple experiments in a single run. Fragment, Mate-Pair and Paired-end library construction is available to facilitate characterization of the entire genome, transcriptome and epigenome, with specific applications including targeted resequencing, whole genome resequencing, small RNA analysis, gene expression analysis, chromatin immunoprecipitation and methylation analysis.
The Roche GS FLX Sequencer utilizes Pyrosequencing to produce millions of long reads with exceptional accuracy in a single run. The instrument is capable of sequencing 300-560 Mb, with reads lengths of 300-450 nt. Reads can be multiplexed using 12 or more individual ‘MID’ tags. Shotgun or Mate pair libraries spanning insert sizes of up to 20 kb can be constructed. A GS-FLX picotiter plate can be divided into 2,4,8, or 16 regions.

The Ion Torrent Personal Genome Machine (PGM) pairs natural sequencing chemistry with semiconductor technology resulting in a revolutionary sequencing process without fluorescence, enzymatic cascades, or optics. When a polymerase incorporates a nucleotide into a strand of DNA, a hydrogen ion is released resulting in a pH change. Ion Torrent captures this process in a massively parallel way using DNA loaded Ion Spheres on a high density array of wells atop a proprietary Ion sensor.
The flexiVent is a computer-controlled mechanical ventilator that measures respiratory mechanics. It can be integrated with the Aeroneb ultrasonic nebulizer that directly mounts onto the unit and delivers broncho-reactive agents deep into the lungs to test AHR (airway hypertension). The flexiVent uses indirect measuring techniques that offers complete control over; timing of the challenge, the nebulization rate and the manner in which aerosolization is synchronized with ventilation. The combination of these controlled experimental conditions, the flexiVent’s advanced indirect measurement techniques, and customized computer programs results in highly reproducible measurements with outstanding accuracy.


The Genetics Core is equipped with several instruments to assist in the extraction of DNA and RNA from blood and tissues. The Autopure LS from Qiagen fully automates the extraction of DNA from fresh and frozen blood, buffy coat, Oragene Kits, cell lysayes and more using the proven Pure Gene chemistry. Automation reduces the handling of potentially infectious samples. For high-throughput extractions the BioRobot Universal completely automates the processing of PAXgene-96, and other 96-well kits from Qiagen. The QiaCube provides walk-away automation of Qiagen’s mini-column format nucleic extraction kits. Personnel in the Genetics Core can assist you with any of these technologies.