About collaborations

Q: How do I initiate a collaboration project?
A: You should download the Gene Expression Profiling proposal form (Word Document).  Please submit the proposal electronically to .

Q: When is the deadline for proposal submission?
A: The proposal will be evaluated and prioritized continuously, so there is no deadline for the proposal submission.

Q: How long does it take to evaluate my proposal?
A: It usually takes 4-8 weeks to evaluate the proposal.

Q: How many chips I can request in my proposal?
A: It depends on your project. Since a chip experiment is very expensive, we do use the chip number requested as one of the selection and prioritization criteria. However, if your project will suffer due to the lack of the appropriate controls and time points, please do not sacrifice the quality of the science you are doing. For those big projects, we suggest you divide your full proposal to several smaller projects and conduct a pilot study first.

Q: How much RNA do I need for each chip experiment?
A: For GeneChip® experiments, we need 40 micrograms for each sample. For cDNA microarrays, we need 200 mg for each sample if duplicates are required.  You will need to provide more material if a universal control is used for a cDNA microarray experiment.

Q: How much does it cost for each chip experiment?
A: For collaborative projects, we will pick up the cost of the sample labelling, chip and hybridization reactions. So, it is free of charge. We do not provide service and we do not retail our chips.

Q: Do you have a recommended protocol for RNA preparation?
A: Yes, we will send the recommended protocol to you once your proposal is approved.

Q: How long would it take to complete my project?
A: It depends on how big is your project. For a project with less than 20 chip experiments, it usually takes 2-4 weeks to complete the project after we receive the samples.

Q: Do you run duplicates for my project?
A: We normally do not run technical duplicates for the GeneChip® experiments. This is based on our reproducibility studies. We concluded the technical variation is much smaller than biological variations in the experiments. To minimize the biological variations, we suggest that you pool your biological samples collected from different individual plants, or even the same treatment collected from different repeated experiments. We run biological duplicates for selected projects upon approval.

Q: My RNA samples are ready. How do I ship my samples?
A: You should ship your samples by express mail. You may use FedEX or UPS for domestic shipment. For international shipment, we recommend World Courier (see below). Please read the recommended shipment instructions e-mailed to you previously.
For items being imported to the United States, shipment delays can be avoided by supplying the appropriate information for review by the USDA Inspector at the port of arrival. The relevant guidelines are detailed here.

You should also send the DETAILED sample information according to the following template. We will not be able to conduct experiments until the DETAILED sample information for ALL of your samples is in the database. You will need to enter the sample information for each of your samples using the template.  You should also send an to us when you send in your samples, so we know to expect your samples.

Q: I have many samples, is there any easy way to enter the sample information for each of the samples?
A: You can use the template function during your online sample information submission process. After you submit the information for the first sample, you can use that as your template for other samples. Be sure to modify the previous sample information before you submit when you use this function.

Q: What is the project ID, sample ID, and Scan ID?
A: A project ID is an ID we issue after your proposal is approved. You need a project ID to login to our sample submission page. A sample ID is the code you obtain after each sample information submission. You should label your samples with your sample ID. You should have a sample ID for each of your samples. Scan ID is the ID we use to identify each unique chip data set.

Q: What is the mailing address for the shipment?
A: The mailing address is , Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA. Tel: (919) 597-3075. The country code for the U.S.A. is +1.

Q: Do you have a recommended international shipment courier?
A: We recommend World Courier, Inc. 55 New Montgomery St., Ste 812, San Francisco, CA 94105. It has offices through out the world. Please check local listings for office and contact information.

Q: How should I label my sample in the international shipment?
A: Please label your samples as "total RNA, non-viable plant materials". Please allow 3-4 days for international delivery, so add enough dry ice.
 

Q: What do I get after the collaborative project is completed?
A: Data may be downloaded from our website. Login as a collaborator and then use the tools available there. You may also contact us for detailed analyses.

Q: Can I get some advice from you on how to analyze my data?
A: Sure. In fact we encourage you to further collaborate with us in data analysis and data mining. We use different algorithms developed by commercial companies, academia, and our internal experts to analyze the microarray data. We aim to identify and use the most stable expression pattern for further knowledge-based discovery. We also have a large microarray database for tracing gene responses under different conditions.