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Facility and Major Equipment


Facility Description:

Laboratory:
The Genomics and Microarray Core Facility at the University of Colorado Anschutz Medical Campus has over 1580 square feet of lab space. The director of the core maintains an office and conference room adjacent to the lab space.

Personnel:
The Genomics Core has 11 team members including Dr. Bifeng Gao (Core Director), Katrina Diener (Core Manager), 7 full time PRAs, and 2 part time PRAs (webmaster 25%, IT 10%).

Computers:
In addition to over 20 Dell and HP desktop computers, the facility is equipped with the following server computers:
  • Illumina HiSEQ NGS data processing server: 40TB hard drive array comprised of four (4x) Dell PowerEdge R610 Servers - each server node containing eight CPU quad cores at 2.27GHz and 48GB RAM 
  • Four additional compute nodes: dual Intel Hex-croes (24 cores each) with 128GB RAM 
  • All compute nodes are 1Gb/s interface and 10Gb/s between storage nodes
  • Illumina Hiseq NGS data storage arrays: two (2x) 100TB hard drive array – each array containing six CPU hex cores and 32GB RAM, and 100TB reserve space available 
  • 480TB of near on-line tape backup (quantum i80 dual LTO-6) with unlimited off-line storage
  • Illumina HiSEQ NGS data storage arrays: two (2x) 100TB hard drive array - each array containing six CPU hex cores and 32GB RAM
  • Illumina Hiseq NGS data transfer (SFTP) server: 10TB hard drive array, four CPU quad cores at 3.2GHz, and 24GB RAM 
  • Dell Precision T7500 Server for Ion Torrent PGM system: 12TB hard drive array, six CPU hex cores at 2.67GHz, and 48GB RAM
 
Bioinformatics Support: The core offers bioinformatics packages for microarray and next generation sequencing data analysis including:
  • Affymetrix GeneChip Command Console
  • Illumina iScan Control Software
  • Genome Studio
  • Ingenuity Pathway Analysis Software by Ingenuity
  • Genomics Suite by Partek
  • Sequencing Control Software, SAV Viewer by Illumina
  • BaseSpace by Illumina
  • Open source and custom scripting for sequencing data 
  • SOMASUITE for SomaLogic proteomic data analysis

Platforms:

Theresa Pacheco 

The Illumina MiSeq System combines proven sequencing by synthesis (SBS) reversible terminator chemistry technology with a workflow that enables cluster generation, sequencing, and base calling in 5 ~ 65 hours runtime. It uses a single flowcell single lane format. With the v3 reagents, it is capable to deliver up to 15 Gb information with 25 million sequencing reads and 2x300 bp read lengths. Sample prep kits are optimized for a variety of applications, such as small genome, amplicons, targeted gene panel sequencing. See more detail on Illumina website.


Tim Garrington 

The illumina HiSEQ4000 System offers the highest daily throughput and lowest price per sample across multiple applications. The dual-flow cell HiSeq 4000 System generates > 400 Gb per day and up to 1.5 Tb per run in 3.5 days. This power allows sequencing of more samples at greater depth, generating richer, more meaningful data in less time. Taking advantage of the innovative patterned flow cell technology first introduced in the HiSeq X Ten System, the HiSeq 4000 System offers an exceptional level of throughput. Patterned flow cells contain billions of nanowells at fixed locations. The structured organization of the flow cell provides for even cluster spacing and uniform feature size, enabling accurate resolution of flow cells clustered at extremely high densities.See more detail on iIllumina website.

Tim Garrington 

The Illumina HiSeq2500 System is a powerful and efficient ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. The regular high output run mode, utilize two flowcell with each flowcell consisting of 8 lanes. With the newest chemistry (v4), the high output run mode is capable to deliver up to 1 Tb information per run with 2 billion sequencing reads and 2x125 bp read lengths. The rapid run mode, which utilize one flowcell with 2 lanes per run format, is capable to deliver up to 180 Gb information per run with 300 million sequencing reads and 2x150 bp read lengths in 40 hours runtime. See more detail on Illumina website.

Ana Oton 

The Illumina iScan system utilizes BeadArray microarray technology for a broad range of DNA and RNA analysis applications. Each bead on Illumina arrays is covered with hundreds of thousands of copies of specific oligos that act as the capture sequences in one of our array-based assays. iScan systems possess the advanced laser and optics components capable of handling even the highest density multi-sample arrays, producing high-quality data with rapid turnaround times. See more details on Illumina website.

Rajesh Agarwal 

The Affymetrix GeneChip scanner 3000 7G is a 16-bit resolution data acquisition confocal scanner which measures fluorescence intensity emitted by the labeled cRNA/cDNA bound to the probe arrays. It uses a high-quality, solid state 532nm Green Laser and the optics are designed to condition the laser beam to deliver an excitation spot size of 3.5 μm. See more details on the Affymetrix website.

Tom Purcell, MD 


Affymetrix GeneTitan system supports gene expression for human, mouse and rat samples on 16-, 24-, 96-array layouts and genotyping studies for human samples on 96- and 384-array layouts. See more details on the Affymetrix website.
 

The Ion Torrent PGM System combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. Direct, real time sequencing detection provides sequencing results typically in less than 3 hours. The Ion PGM™ System supports up to 400–base reads. See more details on the Life Technologies website


Sonia Okuyama, MD 

The Agilent SureScan Microarray Scanner is a laser induced fluorescence scanner designed to read microarrays printed on a standard 1 inch x 3 inch glass slides. It measures the fluorescence intensity of two dyes simultaneously from labeled sample nucleic acid bound to microarrays. See more details on the Agilent website.


Sonia Okuyama, MD 

Covaris S220 Ultrasonicator utilizes an Adaptive Focused Acoustic (AFA) technology to delivers controlled energy precisely and accurately to sample volumes from 25 μl to 10 ml. When operated at higher intensity levels, the instrument can create a tunable shock wave environment with subsequent shear jet forces which has been demonstrated to be ideal for tissue disruption and DNA fragmentation applications. See more details on the Covaris website.

Sonia Okuyama, MD 

The Agilent 2100 electrophoresis bioanalyzer is a microfluidics-based platform for the analysis of RNA, DNA and protein. It delivers high quality digital data using minimal sample. See more details on the Agilent website.


Sonia Okuyama, MD 

The Agilent 2200 TapeStation system is a tape-based platform for RNA, DNA quality control. It provides simpler, faster and more reproducible data through minimal manual intervention using the pre-packaged assay ScreenTape. See more details on the Agilent website.


Sonia Okuyama, MD 

The Agilent 4200 TapeStation system offers automated sample processing using ready to use ScreenTape technology for quick and reliable sample quality control within any Next Generation Sequencing (NGS), microarray (aCGH) or quantitative PCR (qPCR) workflow. The system offers fully automated sample processing for up to 96 samples producing reliable results in as little as 1-2 minutes per sample.

Sonia Okuyama, MD 

SomaLogic SOMAscan™ assay is a new proteomics research tool for life science research, discoveries of protein biomarkers for diagnostics and drug development. The current version of the assay is capable of measuring 1129 human proteins using 50 ul of plasma or serum samples. The protein quantification is fulfilled by SOMAmer (Slow Off-rate Modified Aptamer) reagents, which has unique nucleotide sequences recognizable by specific DNA hybridization probes and are also chemically modified to form three-dimensional structure to provide protein-binding specificity. The SOMAscan assay measures native proteins in complex matrices by transforming each individual protein concentration into a corresponding SOMAmer reagent concentration. The SOMAmer reagent concentration is then quantified by DNA microarray. For more information, please see SOMAscan™ assay.