Descriptions & Applications
We operate from a philosophy of providing the best solutions and service to our customers and collaborators. Thus, we base our investment decisions for technology solutions that best fit the genomic needs of our partners, regardless of the company platform. We currently operate NGS platforms from Illumina, Thermo, 10x Genomics, and WaferGen. This flexibility enables us to match the best sequencing pipeline to our customers’ needs.
Sequencers and Genomic Platforms
- Illumina HiSeq 2500
- Illumina MiSeq
- Thermo Ion S5 XL (Qty2)
- Thermo Ion PGM
- 10X Genomics Single Cell Platform
- Wafergen Single Cell Platform
Molecular Biology and Supporting Instruments
- Illumia cBot2
- Thermo Ion Chef (Qty3)
- BioAnalyzer (Agilent)
- Fragment Analyzer (AATI)
- QuantStudio 7 - qPCR (Thermo)
- Covaris S2 (Qty2)
- Bead Beater
- Plate Reader
- Sanger Sequencers – 3730XL and 3130 (Thermo)
Automated Sample Handling and QA/QC
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 liquid handling tasks including sample normalization , PCR reaction setup, PCR clean up.. One run ranges from 1 to 5 hours.
AutoPure LS is used for large-scale genomic DNA extraction from clinical samples such as whole blood, buffy coat etc. One run (16 samples) usually requires less than 4 hours.
Agilent Bioanalyzer is used for rapid quantitation and quality assessment on DNA/RNA samples including PCR products.
Multiplex SNP Genotyping
Illumina's BeadXpress reader is supported at the Center for medium-throughput, targeted genotyping projects, allowing 96 or 384 multiplexed SNP assays using GoldenGate chemistry on Veracode beads with samples in the 96-well plate format. One run takes 2-3 days. GoldenGate assays for gene expression, DNA methylation, and protein analysis are also available.
Capillary DNA Sequencing
Capillary DNA sequencing at the Center is carried out on an Applied Biosystems 96-capillary 3730XL DNA analyzer, which is the most advanced capillary sequencing platform available today, using the BigDye Terminator v3.1 cycle sequencing chemistry. High quality reads up to 800 nt can be routinely achieved. One run can usually be finished in 24 hrs.
Data Storage
Genotyping, sequencing, gene expression or next-generation sequencing can be intensive and generate massive amount of data. The Center has its own computer resources and will provide short term data storage and will work with investigators on specific data transfer plans for the projects.