Microarray analysis
The Genomics core offers the Codelink microarray platform to Texas A&M investigators. The CodeLink system has been an established platform in our core for several years.
Microarray services include:
- RNA Quality analysis
- Target cRNA synthesis
- Bioarray hybridization
- Image acquisition and processing
- Expression confirmation via real-time PCR
Order CodeLink Arrays from Applied Microarrays (480-775-6320 x2344).
Use Quote #71371
| Catalog Number | Description | A&M Price |
|---|---|---|
| 300031-6pk | CodeLink Rat Whole Genome-6 pk | $592.50 |
| 300026-6pk | CodeLink Human Whole Genome- 6 pk | $592.50 |
| 300033-6pk | CodeLink Mouse Whole Genome- 6 pk | $592.50 |
RNA processing cost payable to the Genomics Core - $180 for CERH members.
$230 for Non-CERH members.
Cost includes quality assessment of starting RNA sample, labeled cRNA preparation, hybridization and preparation of Excel spreadsheet containing raw and normalized data. Data in Gene Spring format can also be provided on request.
Sample Submission
Approximate time from sample submission to data acquisition is 7-10 business days.
Investigators will be responsible for submission of RNA and arrays. All samples and array packaging should be clearly labeled with sample name and contact information. RNA quality and concentration should be verified prior to submission.
Sample Requirements
Sample Requirements
A single aliquot of RNA will be necessary per sample. This will be used for the synthesis of labeled target and for RNA quality analysis.
- For target preparation from total RNA: 3 µg of RNA at a 200-500 ng/µl concentration in nuclease-free water is requested.
- For target preparation from mRNA: 100 ng of mRNA in 10 µl of nuclease-free water is required.
We are able to accommodate special circumstances, such as limiting amounts of RNA. Please call to discuss your specific situation with Laurie Davidson (845-0448).
For detailed protocol information, please visit the Applied Microarrays web site.
RNA Quality Analysis
All samples will be analyzed on an Agilent Technologies 2100 Bioanalyzer. The investigator will be notified of RNA quality.
Sample Processing
RNA that has passed the Agilent Technologies 2100 Bioanalyzer quality control test will be used to generate biotin-labeled cRNA via a modified Eberwine RNA amplification protocol.
Labeled cRNA is applied to the bioarray and incubated for 18 hours. After incubation the slide is washed, stained, and scanned.
Data Acquisition
Array images are processed using CodeLink software. Sample data is returned as a Microsoft Excel workbook with raw and normalized values. This data may be imported into a number of data mining software packages for further analysis. Upon request, data can also be provided in Genespring format. To access your data from the CERH server follow these instructions:
For assistance with array data analysis, please contact Dr. Robert Chapkin .
Minimum Information About a Microarray Experiment (MIAME)
MIAME is a set of guidelines intended to develop a standardized protocol for reporting microarray data. Detailed information regarding MIAME can be found on the Microarray Gene Expression Data (MGED) Society web site ( www.mged.org ). The core service will provide investigators with information pertaining to the arrays, sample labeling, array hybridization, and data acquisition. It is the responsibility of the investigator to synthesize this information with the experimental design in order to fulfill the remainder of the MIAME requirements. MIAME compliance may be required for experiment publication.
Contact Information:Director
Dr. Robert Chapkin
321 Kleberg Center
TAMU 2253
Tel: (979) 845-0419
Email: r-chapkin@tamu.edu
Coordinator
Dr. Laurie Davidson
321 Kleberg Center
TAMU 2253
(979) 845-0448
(979) 862-2378 (fax)
Email: L-davidson@tamu.edu
Jennifer Goldsby, M.S.
Research Associate
323 Kleberg Center
TAMU 2253
(979) 845-3908
jsgoldsby@tamu.edu