RNA Gene Expression Profiling: The following are some organisms the GeneChip Microarray Core can provide expression profiling for using Affymetrix arrays:
Arabidopsis |
Human |
Soybean |
B. subtilis |
Maize |
Vitis vinifera (Grape) |
Barley |
Mouse |
Wheat |
Bovine |
P. aeruginosa |
Xenopus laevis |
C. elegans |
Plasmodium/Anopheles |
Yeast |
Canine |
Porcine |
Zebrafish |
Chicken |
Rat |
NimbleExpress™ Custom Arrays |
Drosophila |
Rice |
CustomExpress® Array Program |
E. coli |
S. aureus |
Human Exon arrays |
| Human Tiling Array Set (14 chips) |
Human Cancer Array |
Mouse Tiling Array Set (14 chips) |
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 200 ng of total RNA. For smaller scales, the Core can offer an alternative labeling protocol called 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.
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