Genomic Core Research Facilities at Cornell
Outstanding, state-of-the-art Genomics shared core facilities are provided by Cornell's Life Science Core Laboratories Center (CLC) which maintains an array of genomics, proteomics, imaging and informatics shared research resources and Core Laboratory services to the university community. The Genomics Core, in collaboration with the CLC Epigenomics, Bioinformatics and Bio-IT cores, provides project consultation, sample preparation, data generation, project consultation and analysis support services for a wide range of applications, including de novo and reference based genome assembly, detection of genetic variation, transcriptome sequencing, small RNA profiling, and genome-wide epigenomic measurements of methylation and protein-nucleic acid interactions. The Genomics Core provides expertise in high throughput sequencing (Ilumina HiSeq 2000 and Roche 454 GS FLX), genotyping and targeted array capture, and has established sample handling methods, LIMS tools and BioHPC informatics analysis pipelines in support of next generation sequencing technologies. The Epigenomics Core provides sample preparation and analysis services for methylation and nucleic acid-protein association studies. The Bioinformatics Core, named the Computational Biology Services Unit (CBSU), is one of ten Microsoft designated High Performance Computing Institutes worldwide. The CBSU has clusters with >600 nodes and 1200 CPUs to support analysis, has expertise in large scale sequencing data management, and offers informatics pipelines for 454 and Illumina data. The goal of the facility is to provide rapid and accurate genomics services on a cost-effective fee-for-service basis.
Next Generation DNA Sequencing Technologies: The Genomics Core has two Illumina HiSeq 2000, an Illumina GAIIx, and a Roche 454 GS-FLX. Applications on the Illumina sequencers include genomic and amplicon resequencing projects, ChIP- Seq, digital gene expression, whole transcriptome, and small RNA analysis projects. Applications on the 454 GS-FLX include de novo genomic and transcriptome sequencing and metagenomic discovery projects.
DNA Sanger Sequencing: The facility provides DNA sequencing of plasmids and PCR products using two ABI 3730xl instruments. We also accept plates of user-performed cycle-sequencing reactions for analysis. Average data return time is less than 30 hours. Sample submission, tracking, data retrieval and billing are integrated into a web based laboratory information management system (LIMS). All samples are barcoded, processed using robotic liquid handling systems, and tracked by the LIMS.
Genotyping: Genotyping services are available using the ABI 3730xl for DNA fragment analysis, with up to five-dye detection for microsatellites. An Illumina BeadXpress instrument is available for up to 384-plex, custom SNP genotyping projects. The Illumina BeadArray and Affymetrix microarray platforms are available for custom SNP genotyping panels and whole genome association studies with up to ~1 million SNPs per sample, with LOH and copy number variation (CNV) analysis. A Sequenom Compact mass spectrometer is available for up to 40-plex SNP genotyping. An ABI Viia7 instrument provides real-time PCR for quantitative gene expression and SNP genotyping.
Epigenomics: Quantitative DNA methylation analysis on the Sequenom Compact mass spectrometer and on NimbleGen microarrays is available in collaboration with the CLC Epigenomics Facility. DNA methylation profiling and ChIP- Seq analysis are available on the Illumina and 454 GS-FLX sequencers.
Gene Expression: Gene expression analysis is available using the sequencing platforms and the Agilent, Illumina and Affymetrix microarray platforms. An AB Viia7 is available for sequence detection system for real-time PCR analysis.
Other Core Laboratories at Cornell include:
- Proteomics and Mass Spectrometry, which provides with cutting-edge technologies in mass spectrometry and proteomics including consultation, support, training and technology for the identification and characterization of proteins and peptides and their modifications.
- Microscopy and Imaging Core where researchers have access to confocal microscopy, transmitted and fluorescence light microscopy, molecular imaging (whole mouse luminescence and fluorescence imaging) and high-resolution ultrasonic imaging, as well as prototyping and analysis tools such as stereo microscopes, a spectrofluorometer and image processing software. We provide training on these instruments and general advice on digital imaging, image analysis, live cell microscopy, tissue and animal imaging and fluorescence techniques and measurements.
- Additional facilities across campus are listed here.