Functional Genomics - Equipment
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. The cDNA array platform is operated using a Gene Machine Omnigrid arrayer. Printed and hybridized cDNA slides are scanned and analyzed using a GenePix 4000B scanner from Axon Instruments. Additional equipment used for cDNA plate production includes a Biomek FX Liquid Handling station from Beckman Coulter, a Gel Doc 2000 gel imaging system from Bio Rad and a GENios plate reader from Tecan. Submitted RNA samples are quality-checked using an Agilent 2100 Bioanalyzer and NanoDrop ND-1000 spectrophotometer. A GMS 417 Arrayer is available for special projects (e.g., antibody slides) and as a backup. The Illumina BeadXpress Reader is used for expression analysis, SNP genotyping and protein-based assays. When appropriate, microarray data is validated using the Agilent Technologies Stratagene Mx3005P QPCR System.
Next Generation Sequencing Technologies: To provide Next Generation sequencing technologies to its researchers, CINJ has acquired or secured access to a comprehensive suite of technologies through cooperative agreements with each of its consortium member institutions (RWJMS, Rutgers University, Princeton University). For example, EOHSI (Rutgers, RWJMS) recently acquired a Roche/454 Genome Sequencer FLX System pyrosequencing platform for use by members of the NIEHS funded Center for Environmental Exposure and Disease (CEED). As Director of the CEED as well as the Functional Genomics Shared Resource, Dr. Zarbl was able to negotiate that the Roche/454 FLX System be integrated into the Functional Genomics Shared Resource. The Functional Genomics staff have already obtained training on the instrument.
CINJ has also put in place a cooperative agreement to provide researchers access to the NGS technologies available at the Waksman Genomics Core Facility (Rutgers, Piscataway). In March of 2008, the Waksman facility acquired a Life Technologies (Applied Biosystems) Sequence by Oligonucleotide Ligation and Detection (SOLiD) Genome Analyzer. The SOLiD has been upgraded to version 4 and is currently capable of generating 100-140 gigabases of sequence. Current protocols support fragment (50 bp), paired-end (50 bp+35 bp), or mate-pair (50 bp+50 bp) sequence in 7-12 days. In December of 2009, an Illumina Genome Analyzer IIx was installed in the lab. The Illumina is capable of generating single or paired-end reads of 150bp, which corresponds to a maximum throughput of 45-90 gigabases of sequence in 4-10 days. Both the SOLiD and Illumina instruments are housed in an environmentally controlled lab and operated by Dr. Sidote and his staff. Auxiliary equipment for the Genome Analyzers includes two nanodrop spectrophotometers, a Covaris acoustic DNA sonicator, a GeneMachines DNA HydroShear, IKA vortex mixer, and a cBot cluster generation system.
The rapid technological advances and growing demand for these capabilities by CINJ 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.