Research Technologies Branch

RML Research Technologies Section

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 all custom Affymetrix technologiess; (3) high-throughput SNP and TaqMan (Q-RtPCR) analysis; (4) human and pathogen 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 capillary-basedsequencing capacity is greater than 1 million bases every 12 hours. We provide access to this data using the Finch database: a set of sequencing servers that process and store the DNA sequence data, and also house genomic sequence. For more information contact Steve Porcella or Kent Barbian.

Genome Sequencing

The Genomics Unit performs and manages contract and in-house (SOLID) high-throughput DNA sequencing of enkayotic, prokaryotic and viral genomes. For info, contact Steve Porcella.

ERGO Genome Database

The ERGO Genome Database is a graphics-intensive database for the storage, analysis and presentation of genome data. Available for interactive analysis are 1,404 prokaryote and eukaryote genomes.

• More than 1,404 genomes in database
• Graphical interface
• Gene context
• Biochemical pathways
• Functional annotation
• Comparative analysis
• Search tools
• Regular updates

Microarray

The Genomics Unit performs statistically sound microarray experimental design, design of high density Affymetrix arrays, and complete data analysis. E-mail Steve Porcella for more information.

Affymetrix GeneChip Arrays

• Support for all commercial Affymetrix GeneChips (Mouse, Human, SNPs, S/T, etc.)
• Support for 8 custom pathogen chips containing >60 different pathogen genomes.
• If you want your organism on a custom chip, contact Steve Porcella to discuss.

General Microarray Assistance

• Balanced experimental design for maximum statistical power
• Support for RNA isolation, labeling, and hybridization
• Support for microarray data analysis and bioinformatics:
• 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
• Data submission and publication-quality figures and tables.

Human (Host) and Pathogen Genotyping

• Gene resequencing; exon/intron boudaries, exons, and 5’ untranslated regions
• SNPlex; High throughput multiplex analysis of known SNPs across 1000’s of patient DNAs
• Allelic discrimination; High throughput Taqman-based assay, low cost, for analyis of know SNPs across patient cohorts.
• Affymetrix human 6.0 SNP chip, copy number analysis
• Affimetrix MIP technology-malaria SNP Chip 3,000-10,000 SNPs analyzed across Plasmadium genome for malarial blood draws and lab isolates.

High Throughput QPCR

The Genomics Unit performs high-throughput QPCR assays for focused gene set analysis, and microarray data validation. 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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