About collaborations

Q: How do I initiate a collaboration project?
A: You should download the Gene Expression Profiling proposal form. Please submit the proposal electronically to Tong Zhu. Although it is not strictly necessary, we encourage you to identify a Syngenta researcher to sponsor your proposal.

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. Please ensure the quality of the experimental design as well as the control of the cost. For those big projects, we suggest you divide your full proposal to several smaller projects and conduct a pilot study first.

About profiling experiments

Q: How much sample do I need for each chip experiment?
A: For expression analysis, we need 40 micrograms of total RNA for routine analysis using one cycle amplification protocol. We will reduce quantity requirements based on special request. In those cases, a two cycle amplification protocol will be used to prepare labeled targets. For DNA hybridization experiments, a total of 20 microgram of genomic DNA is needed.

Q: How much does it cost for each chip experiment?
A: For collaborative projects, we will pick up the cost of the sample labeling, 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 and DNA preparation?
A: Yes. We recommend using Ambion’s Tri Reagent® for RNA preparation, and CTAB protocol followed by RNase treatment for DNA preparation.

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: Yes, but we recommend running only biological replicates. 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 to form your biological replicates.. Based on our reproducibility studies we normally do not run technical replicates in GeneChip® experiments; data indicate that technical variation is much smaller than biological variations in these experiments.

About sample submission and shipment

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 e-mail message to us when you send in your samples, so we know to expect your samples.

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 Tong Zhu, Syngenta Biotechnology Inc., 3054 East Cornwallis Road, Research Triangle Park, NC 27709-2257, USA. Tel: +1 (919) 597-3075.

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 throughout 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.

About data and data analysis

Q: What do I get after the experiment is completed?
A: Data will be mailed to you in a CD within a week.

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 diverse 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.

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