Service Title
Gene ST assay
Workflow Code
Affy_GST
Short Service Description
An expression array that offers whole transcript coverage. Smaller format of the array makes it a cost-effective expression profiling solution. Human, rat and mouse arrays only
Base Price (Price per unit)
Price on enquiry
Turn Around Time
5 working days
Detailed Description and background
This assay system incorporates a subset of Exon ST array probes and includes the most up-to-date well-annotated genes. The probes are distributed across the full length of the transcript therefore providing a more accurate overview of gene expression. The arrays include quality control probes to assess the sample amplification and successful hybridisation to the arrays. A positive control is included to monitor assay performance. Initial analysis is performed in Expression Console. CPGR will provide assistance with experimental design where required.
Service Details
The sample number for analysis is dependent on the nature of the experimental design. It is advisable to have at least 3 replicates however the actual optimum number depends on the samples to be investigated and variance inherent in the experimental system. RNA samples must be of good quality with 260/280 ratios of 1.8-2.1 and 260/230 ratios > 1.8 and non-degraded. The quality of all samples are routinely checked prior to analysis. Sample concentration should be at least 70ng/ul (at least 200ng is required for the assay). Following the QC steps, first and second strand cDNA synthesis will be carried. The double stranded cDNA will be transcribed to aRNA (amplified RNA), followed by another round of 1st strand synthesis to generate sense strand DNA. The single stranded DNA is fragmented and end labelled with biotin prior to hybridisation. Following hybridization, the arrays are washed and stained using the GeneChip Fluidics Station 450 and scanned using the GeneChip® Scanner 3000 7G. The initial analyses is carried out to determine the quality of the data using Expression Console. Bioinformatics support is available if required.
Service Deliverable
Following initial analyses using Affymetrix Expression console, the raw data files are sent to the client with a data QC report. If required, bioinformatics support can be provided.
Sample/Info Submission Info
1 sample per array. At least 500 ng of good quality RNA (in RNAse free water) required at a minimum concentration of 70ng/ul, 260/280 ratios 1.8-2.1 and 260/230 ratios >1.80. Samples should be submitted on dry ice with a sample submission form (this will be sent to the client in advance) providing all the sample details required.
Pricing Details
Price on request
Key Words
Affymetrix, gene expression, gene profiling, Biomarker discovery, array, RNA
Sample Shipping Address
Institute of Infectious Disease and Molecular Medicine, UCT, Faculty of Health Sciences, Wernher and Beit Building, Level 2, Lab S2.09, Anzio Road, Observatory, Cape Town 7925, South Africa
Related services
Bioinformatics
Printable Version
A downloadable PDF Print Version of this service can be found here.
Target Gene Expression
