GeneChip™ Microarray Core: Where To Start

• What is the biological question/hypothesis?

• What is the origin of the samples?

• How will the RNA be extracted

• What chips should I use?

• How many replicates should I use per condition?

• Should I pool samples?

• Can I standardize the experimental manipulations and extraction procedures to minimize variation?

• What comparisons do I wish to make?

• How will I analyze the data?

A number of publications have addressed the design of microarray experiments:

Bolstad et al. Experimental design and low-level analysis of microarray data. Int Rev Neurobiol. 2004;60:25-58.

Leung & Cavalieri. Fundamentals of cDNA microarray data analysis. Trends Genet. 2003:19:649-59

Churchill. Fundamentals of experimental design for cDNA microarrays. Nat Genet. 2002 Dec;32 Suppl:490-5.

Sample pooling for microarray analysis: a statistical; assessment of risks and benefits. Affymetrix tech note 2004

Wei et al. Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics 2004, 5:87

 

A complete listing of all Affymetrix GeneChips is available at www.affymetrix.com/products/arrays/index.affx. Other genomes will be added in the near future through the Affymetrix Consortia Program. Custom target genome arrays can be produced by NimbleGen through the NimbleExpress program or by Affymetrix through the CustomExpress program. The tiling array sets can be used to identify novel RNA transcripts throughout the genome. The Exon arrays sample 1.4 million predicted exons in the human genome and can be used to study alternative splicing.

The Core can also provide expression profiling for the following organisms using NimbleGen arrays.

• Arabidopsis thaliana
• Homo sapiens
• Saccharomyces cerevisiae
• Drosophila melanogaster
• Rattus norvegicus
• Mus musculus
• Zebrafish
• > 125 prokaryote genomes

A catalog listing all available NimblGen arrays is available.

The Core can also profile miRNA expression using commercially available arrays from Exiqon and Invitrogen.

The standard Affymetrix protocol using one round of in-vitro transcription amplification requires 5 µg of total RNA. For smaller scales, the Core can offer alternative labeling protocols using two rounds of IVT (Ambion GeneAmp II, Arcturus RiboAmp HS) or the novel SPIA technology (Nugen Ovation).

DNA Genetic and Chromosomal Analysis : The Core can provide DNA-based analyses using the following Affymetrix chips:

GenFlex Tag Array

SNP Mapping 10K Array

SNP Mapping 10K 2.0 Array

SNP Mapping 100K Set (2 chips)

SNP Mapping 500K Set (2 chips)

SARS Resequencing Array

Mitochondrial Resequencing Array

CustomSeq™ Array Programs

CustomSeq™ Resequencing Arrays

ENCODE01 Array

The SNP mapping arrays can be used for linkage and genome association studies, as well as loss-of-heterozygosity and comparative genomic hybridization. The tiling arrays can be used for localization of transcription factor binding, transcript mapping, and exon definition.

The Core can also provide the following tilling arrays from NimbleGen:

ENCODE ChIP-chip

Human Genome Tiling chip set (38 chips)

Mouse Genome Tiling chip set (37 chips)

Human 1.5Kb ChIP

Human 5Kb ChIP (2 chips)

Mouse 1.5Kb ChIP

Mouse 5Kb ChIP (2 chips)

Human Whole Genome Array CGH

Mouse Whole Genome Array CGH

C-elegans Whole Genome Array CGH

Human Chr X Fine Tiling

Custom Fine Tiling Array CGH

 

Real-time Quantitative PCR : For Microarray data validation and Q-PCR services please visit CFAR website at http://cfar.ucsd.edu/genomics/

Genome Sequencing: The GS FLX System by Roche provides a combination of long reads, exceptional accuracy and high throughput. The System supports the sequencing of samples from a variety of starting materials, including genomic DNA, PCR products, BACs, and cDNA.