Functional Genomics - Equipment

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Next Generation Sequencing Technologies:

Nucleic Acid Extraction for Analysis
Qiagen Autopure(s) – Large volume whole blood and cell pellet DNA extractions (salting out)

QiaSymphony(s) – CLIA lab instruments for DNA/RNA extraction from any tissue source (bead based)

Qiagen Universal(s) – Solid phase extraction instruments for high throughput projects

Qiagen EZ1(s) – Extractions from samples with limiting starting materials (bead based)

Hamilton ChemagicSTAR(s) – Low to high volume extractions for both liquid and solid biomaterials. Optimized protocols for difficult tissue types (bead based)

Hamilton EasyBlood(s) – Automated blood fractionation for plasma/serum separation and cell layer preparation for extraction/culture

Genotyping/Gene Expression by QPCR
Life Tech ViiA™ 7 Real Time PCR Instrument(s) – Quantitative real time PCR for genotyping and gene expression applications

Fluidigm BioMark™ System(s) – Capable of 9,200 genotypes in picoliter volumes in 90 min; high throughput genotyping and gene expression

Fluidigm EP1 – High throughput genotyping measurements. Capable of 100,000 genotype calls and hour.

Fluidigm C1 – Automated single cell processing for genotyping and gene expression

Wafergen™ SmartChip System – capable of 5000+ genotypes in any sample or assay format desired

Microarrays for Genotyping, Gene Expression, Array CGH, Methylation, CNV analyses
Affymetrix GeneChip® Systems – Affymetrix cartridge arrays (catalogue or custom)

Affymetrix GeneTitan®(s) – High throughput array analysis of 96 microarrays in 24hrs.

Illumina iScan System – Genotyping and Gene Expression analysis for all catalogue and commercial Illumina bead arrays

NextGen Sample Prep, Library Prep and Sequencing
NuGEN Mondrian(s) – Fully automated NextGen library preparation for sequencing ready products

Caliper SciClone(s) - Fully automated construction of sequencing libraries (high throughput).  Automated target enrichment protocols for exome, cancer panel and other targeted sequencing applications

Caliper Zephyr(s) – Fully automated PCR and sample cleanup for NextGen and Sanger sequencing applications

Ion Torrent Personal Genome Machine(s)™ (PGM) – Semi-conductor sequencing for gene sequencing panels and targeted enrichment sequencing

Ion Torrent Proton – Semi-conductor sequencing for high throughput whole exome and whole genome sequencing applications

Illumina MiSeq Personal Sequencer(s) – Targeted enrichment sequencing and disease panel sequencing

Illumina HiSeq 2500(s) - High throughput whole exome and whole genome sequencing applications

Liquid Handling / Automation
Hamilton STAR(s)

Tecan Freedom Evo(s)

Biomek FX(s)

Sample Quality Control (Analytical and Functional)
Caliper LabChip DS(s) – Cuvetteless spectroscopy with cDrop analysis for contaminant profile generation

Caliper LabChip GX(s) – Lab on a chip analysis for nucleic acid sizing and fidelity analysis

Fluidigm technologies (above) – RUIDTM and RUIDGxTM

The rapid technological advances and growing demand for these capabilities by Cancer Institute members requires significant computing and storage capabilities. We are working closely with the Bioinformatics shared resource to deploy scalable, efficient and secure storage and archiving capabilities to ensure seamless flow from data acquisition to storage and processing. This involves increasing the existing computing resources within the Bioinformatics shared resource to meet immediate needs (currently 30TB and projected to grow to 100TB within a year). Based on the anticipated growth in storage needs and the costs involved in deploying and maintaining an in-house solution, we are also exploring new avenues (i.e. based on Cloud Computing) as a cost-efficient, financially and operationally viable option.

DNA Microarray Technologies:

The Affymetrix GeneChip system is controlled by a Dell Optiplex GX150 computer and includes an Agilent Technologies GeneArray Scanner, a GeneChip Fluidics Station 400 and a GeneChip Hybridization Oven 640. We acquired the Agilent Technologies GeneArray Scanner (replacing our older Affymetrix 3000 Scanner) to assure compatibility with newly designed Affymetrix GeneChips. Submitted RNA samples are quality-checked using an Agilent 2100 Bioanalyzer and NanoDrop ND-1000 spectrophotometer.  Microarray results can be validated using the Agilent Technologies Stratagene Mx3005P QPCR System.



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