RNA Gene Expression Profiling: The following website contains the organisms the GeneChip Microarray Core can provide expression profiling for using Affymetrix arrays:
Custom target genome arrays can be produced by NimbleGen. 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 organisms using NimbleGen arrays.
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 100 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:
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™ 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, RNA, and cDNA.
The system is also capable of processing Nimblegen and Agilent Exome Captured samples. Sequence Capture technology is a revolutionary process for the enrichment of selected genomic regions from full complexity human genomic DNA in a single step. Sequence Capture was developed to eliminate the necessity of setting up thousands of PCR reactions, instead allowing for parallel enrichment of target regions in a single experiment.
