Scientific Programs

Complete GeneChip® Instrument System  

The Genomics Core Laboratory supports processing of several types of GeneChip arrays for various genome-wide applications: 3'  expression arrays to quantify transcription;  SNP arrays to detect single nucleotide polymorphisms, exon arrays to assess alternative splicing; and tiling arrays to identify protein-DNA interactions.

Microarray Core Package

The standard Core microarray package includes:
  • quantification and quality control of RNA samples,
  • synthesis of labeled cRNA;
  • GeneChip hybridization and fluorescence quantification;
  • data storage in EDGE database;
  • provision of annotations and standard statistical analysis;
  • provision of quality control metrics.

Users that require additional bioinformatic support should contact the Core staff; help may be provided on a collaborative basis.

DNA Microarray Screening

Overview
Microarray screening is typically used for whole-genome transcriptional profiling. An RNA sample is amplified and converted to labeled cRNA, which is hybridized to a high-density array of oligonucleotide probes. Quantification of the signal intensity of the fluorescent label for each probe provides a measurement of transcript abundance. The Core uses Affymetrix GeneChips for transcriptional profiling; 3' expression arrays are available for a variety of organisms. Additional applications include detection of alternative splicing via exon arrays, and analysis of gene regulation via ChIP-chip on tiling arrays.

Flow chart

User-supplied components

1. Sample: 5 µg total RNA at 500 ng/µL minimum concentration
  - samples that do not meet these standards require additional processing (e.g., two rounds of amplification) by the Core staff; please contact prior to sample submission
2. MIAME sample submission datasheet ( excel form)
3. GeneChip (one per sample)


RNA isolation
High-quality RNA is the single most important component of transcriptional profiling. We have obtained excellent results using the Qiagen RNeasy Mini kit for RNA isolation. RNA that is not immediately isolated from sample material should be stabilized by physical (such as freezing in liquid nitrogen) or chemical (RNAlater for tissue samples, or RNAprotect for harvested cells) methods. Follow the manufacturer's protocols for RNA isolation from particular types of samples (e.g., plant material). For RNA isolated using TRIzol reagent, we recommend an additional purification (such as RNeasy Mini) to remove impurities that can impair the labeling reaction.

Bioinformatics tools

Microarray data, including QC and statistical metrics analysis, are deposited into a web-accessible Oracle database (EDGE, for Effectual Database for Gene Expression). Researchers at NIDDK have access to data analysis software packages through floating licenses. File formatting for either of these programs can be performed directly via the EDGE web interface.

Pricing

The cost for microarray screening is $400 per sample. In addition, the user provides the GeneChips for screening; prices effective as of October 2008 are listed here. Please consult with the Core staff prior to ordering to insure that you obtain the correct GeneChip for your experiment.

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Page last updated: May 31, 2009

General inquiries may be addressed to:
Office of Communications & Public Liaison
NIDDK, NIH
Bldg 31, Rm 9A06
31 Center Drive, MSC 2560
Bethesda, MD 20892-2560
USA
301.496.3583

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