Location
Room B-303: Affymetrix GeneChip system, and Agilent 2100 bioanalyzer.
Room D-309: Illumina Genome Analyzer platform.
Room A-157: Custom array system, TaqMan 7900HT and Illumina Pipeline Server.
Facilities and Services
Affymetrix GeneChip arrays
This platform can analyze all GeneChip probe arrays for gene expression analysis and DNA analysis. A broad range of whole genome arrays are available in Affymetrix product lines, including human genome array, human SNPs, mouse genome, rat genome, rat toxicology, rat neurobiology, drosophila genome, Arabidopsis genome, C. elegant genome, Yeast genome, E. coli and P. aeruginosa genome, and others. We can help you design your experiment and provide detailed protocols for both RNA and DNA sample preparations.
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Custom array service
Custom arrays provide flexibility in the choice of arrayed elements, particularly for the preparation of smaller, customized arrays for specific investigations. The arrayed material can be complementary DNA (cDNA), oligonucleotide probes, and proteins, and the target area may be glass slides, porous nylon membrane, or other microplates. The custom array service supplies the Robotic 96-well/384-well transferring, spotting technology, hybridization and washing system, and an array reader.
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Agilent 2100 Bioanalyzer
This piece of equipment replaces conventional gel electrophoresis and improves analysis of DNA, RNA, proteins and cells through automation for better accuracy and reproducibility, rapid visualization of sample quality and quantity, and high sensitivity with only a small amount of sample. Both RNA Nano and Pico chip kits are available in the core facility.
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Microarray data analysis
Our staff has a great deal of expertise in microarray data analysis. In the past few years, we have evaluated more than 12 software packages including GeneSpring, Spotfire, SAM, dChip, BRB, R-based tools from Bioconductor and some statistical packages, such as R and S-plus, etc. and helped each array user with data manipulation, including data visualization, normalization, statistical analysis and error modeling, pattern recognition, pathway and gene network, and data interpretation meaningful to biologists. We have also started to evaluate the tools and software for SNP data analysis since Affymetrix brought the 10K SNP chip to the research community. The core staff is available for consulting.
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ABI 7900HT Sequence Detection System
In addition to standard PCR thermal cyclers, MCF also houses a real-time PCR instrument. The 7900HT System is the only real-time quantitative PCR system that combines 96- and 384-well plate compatibility and the TaqMan Low Density Array with fully automated robotic loading and also offers optional Fast real-time PCR capability. Using two automation software tools, Plate Utility and Automation Controller, most of the gene expression and SNP genotyping workflow is fully automated for high-throughput applications. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay.
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Illumina Genome Analyzer II (Solexa)
This latest technology is able to produce gigabases of high quality sequence information in a single run, and to support the broadest set of applications, including those used to profile and discover novel transcripts, to create high-resolution genome-wide maps of DNA-protein binding sites and to sequence entire human genomes.
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Contact
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Jenny Xiang, MD Director, Associate Research Professor (212) 746-4258 jzx2002@med.cornell.edu Jian Zhang Senior Research Technician II Room B-303 (212) 746-6238/5076 jiz2009@med.cornell.edu Tomy Thomas Senior Accounting Assistant (212) 746-6503 tthomas@med.cornell.edu |
Dirk Schnappinger, PhD Consultant for spotting array Associate Professor dis2003@med.cornell.edu Wan-Ying Hsieh Senior Research Technician II Room B-303 (212) 746-6238/5076 wah2004@med.cornell.edu |
