The experimental design is critical for generating interpretable data. In general, the biological variability is greater than the technical variability, so replicates should be independent biological experiments. The following is a list of important considerations:
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:
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:
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.
