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Resources
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Genomics Core
Overview:
The purpose of the Genomics Core is to provide microarray-based
technologies measuring genomic expression and protein-DNA interactions.
Mature Technologies
Affymetrix Platform
The Affymetrix platform includes an automated fluidics station that provides highly reproducible washing and
staining, a high-resolution 7th-generation scanner with autoloader, 1.09 micron resolution to accommodate
arrays of 6.5 million probes and automated scanning of up to 48 arrays at a time. The platform is capable
of providing 3' expression array analysis with 11 probe pairs per transcript. Exon arrays are available for
whole transcript labeling for human and mouse. These arrays probe all known and predicted exons to
support gene expression and alternative splicing analyses. The facility also provides genome tiling
arrays with up to 6.5 million probes, available as single-stranded designs for ChIP-chip analysis or
double-stranded designs for transcriptome mapping and profiling. The capacity of the facility is
currently 200 samples per month.
Spotted Array Platform
The spotted array platform includes a Bio-Rad spotter capable of printing in-house arrays with up to
40,000 probes and includes a four laser PerkinElmer scanner with 5 micron resolution. The spotted
array platform provides longer oligonucleotide probe arrays for gene expression, tiled PCR products
for ChIP-chip analysis and custom spotting for specialized projects. The platform is capable of providing
hundreds of arrays per month, and has a scanning capacity of over 250 per month.
Agilent Platform
The Agilent platform leverages the PerkinElmer scanner that is shared with the spotted array platform, along
with an Agilent-specific hybridization oven. The platform supports arrays of up to 244,000 features,
suitable for high-resolution tiling experiments. Slides are also available with up to as many as 8
separately hybridizable arrays on them, providing very cost effective small arrays. Flexibility is a
key advantage of the Agilent platform, allowing custom array content that can be designed online,
with no extra costs for new slide designs. Methods currently used with the Agilent platform are 3' expression,
ChIP-chip, transcriptome mapping and micro RNA expression.
Genome Tiling
Genome tiling array infrastructure has continued to mature, making use of the Affymetrix, Agilent and spotted array platforms. Usage has become more widespread, and informatics efforts have improved the tools available for these data. Specifically, we have supported the Innate Immunity, Halobacterium and Yeast research groups.
Data Software and Centralization
In order to support gene expression and DNA-protein interaction analyses using data generated by the Genomics Core, we ensure that data are analyzed and deposited in a timely manner into the system of integrated databases, providing information access for Center researchers.
Plans:
Specific plans to enhance and expand the capabilities of the Genomics Core include, additional pipelines for exon array analysis, singular value decomposition pipeline, make the method used by Carter et al. (PMID: 16533914) available to other research projects and continue to investigate next-generation sequencing technologies and attempt to obtain this platform in-house.
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Institute for Systems Biology
CSB Home
Center for Systems Biology at the Institute for Systems Biology
