Genomics Unit
Steve Porcella, Chief
The RML Research Technologies Section, Genomics Unit supports five state-of-the-art technologies to meet investigators' ongoing and future needs. The facility provides: (1) standard and custom DNA sequencing from single clones to genomes; (2) support for custom Affymetrix and spotted microarrays; (3) high-throughput SNP and TaqMan (Q-RtPCR) analysis; (4) robotics for genotyping and microsatellite services; and (5) advanced bioinformatics for all of the above. The goal of the unit is to support advanced technologies and provide high-quality service in a timely manner to all NIAID researchers.
Technologies Available
DNA Sequencing
The Genomics Unit performs DNA Sequencing of single or multiple clones, PCR-based DNA sequencing, multi-locus sequencing, and the sequencing of larger fragments. Our current sequencing capacity is greater than 1x106 bases every 12 hours. We provide access to this data using the Finch Sequencing Suite: a set of sequencing servers that process and store the DNA sequence data, and also house genomic sequence.
Production DNA Sequencing Server
This server manages the DNA Sequencing of single or multiple clones, multi-loci sequencing, and the sequencing of larger fragments. For more information contact Steve Porcella or Kent Barbian.
Genome Sequencing Servers
The Genomics Unit performs and manages contract high-throughput DNA sequencing of prokaryotic and viral genomes. The Genomic Sequencing Servers store and analyze the data. For info, contact Steve Porcella.
ERGO Genome Database
The ERGO Genome Database (NIAID only) is a graphics-intensive database for the storage, analysis and presentation of genome data. Available for interactive analysis are 633 prokaryote and eukaryote genomes.
- More than 633 genomes in database
- Graphical interface
- Gene context
- Biochemical pathways
- Functional annotation
- Comparative analysis
- Search tools
- Regular updates
SNPs
We have high-throughput technology for SNP genotyping via allelic discrimination and SNP discovery via DNA sequencing. Our throughput for allelic discrimination is over 13,000 samples a day. Send an e-mail to Steve Porcella for further information regarding SNP services.
Microarray
The Genomics Unit performs statistically sound microarray experimental design, design of high density Affymetrix arrays and spotted arrays, and complete data analysis. E-mail Steve Porcella for more information.
Affymetrix GeneChip Arrays
- Support for all Affymetrix GeneChips (Mouse, Human, etc.)
- A RML custom chip is currently available representing 6 organisms and 21 genomes.
- A second custom RML chip will be available June 1st, 2005.
- There are plans for future custom chips. If you want your organism on a custom chip, contact Steve Porcella to discuss the feasibility.
Custom Spotted Arrays
- DNA and Protein printing on glass and membrane
- 768 spots per hour, 28,416 spots per slide, 3,000 slides per year
- Custom filtering design process specific for each array constructed
- >90% spot and hybridization quality
- >80% TaqMan confirmation (array validation)
General Microarray Assistance
- Balanced experimental design for maximum statistical power
- Support for RNA isolation, labeling, and hybridization
- Microarray data analysis and bioinformatics software support:
- Data normalization, filtration, and reduction to genes of interest
- Log transformation, ratios, histograms, p-values, subgene lists, and clustering
- Annotation and genome versus genome BLAST analysis
- Experimental design and statistical data processing
Taqman
The Genomics Unit performs high-throughput Taqman assays for focused gene set analysis, microarray data validation, and allelic discrimination. Our instrumentation has the capacity to process in triplicate over 3,000 gene expression samples every 24 hours. Please contact Steve Porcella for more information.
Bioinformatics
A wide range of general and specific bioinformatics support for the above technologies is provided by the Genomics Unit. Contact Steve Porcella for further details.
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