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Affymetrix arrays
System
The Leiden Genome Technology Center has two complete Affymetrix systems with scanner, autoloader, hybridization oven, and fluidic stations. One scanner is a GCS-3000-7G; the other is a four color Scanner GCS-3000-7G-TG (Targeted Genotyping System).
We also have access to a GeneTitan™ a fully integrated system that automates array processing from target hybridization to data generation. Ask the LGTC for possibilities.
Arrays & Assays
- DNA
- SNP Genotyping & CNV Analysis - genome-wide human SNP 5.0/6.0 and human 550K mapping assay
- Targeted Genotyping - MIP assay
- Resequencing
- RNA
- Whole transcript expression - exon and gene arrays
- 3' expression - whole genome expression
- microRNA expression profiling
See the Affymetrix website for more information on the Affymetrix technology, assays, and arrays.
Affymetrix at the LGTC
Projects
For first time users: when you have a project for Affymetrix and have no experience with Affymetrix protocols; it is recommended to discuss it with the LGTC. We can help you discuss and evaluate the possibilities, costs, planning, and all other issues.
Quotation
Once it has been decided how to start you will need a quotation from the LGTC. This quotation can be requested via the LGTC order system for which you will need a valid account. A quotation for Affymetrix experiments contains the following products: Affymetrix order charge, Affymetrix arrays, Affymetrix assay or labeling kit, hybridization mix, and hybridization via the LGTC. To accept the costs you need to deliver a printed and signed version of the quotation to the LGTC. Only then, the project will start.
Labeling and/or DNA sample preparation
We do not offer services for the labeling of RNA and at all times, DNA samples have to be prepared by yourself in your own labs. We do not have the necessary equipment.
Sample delivery
Once you are ready to deliver your samples to be hybridized (DNA or labeled cRNA) you need to complete the Affymetrix sample sheet and mail it to info@lgtc.nl mentioning Affymetrix sample sheet in the subject. Without a quotation or sample sheet we will not start processing your samples.
Planning and time span
According to our terms & conditions, results will be delivered four weeks after the delivery of the samples. When unexpected circumstances occur that delays the planning, you will be notified. The project starts when the samples are delivered to the LGTC together with the signed quotation and the sample sheet.
Data and data analysis
The quotation does not include data analysis since the LGTC will not do the data analysis for you. You will receive the raw data either on a DVD for small projects of you can download it from the network for larger projects. We will not keep your data for longer than three months, it is your responsibility to make your own back ups.
For the data analysis of Affymetrix projects the software Comand Console is free to download from the Affymetrix website.
Summary: what can you expect from us? General rules
- Hybridization of samples. The LGTC will do the hybridizations. We will do the hybridizations according to Affymetrix latest protocols. When the run has failed, the LGTC cannot be held responsible and the issue will be dicussed with you. Affymetrix arrays will not be refunded and not re-run for free.
- You are responsible for the data management of your experiments. With the raw data you can do all data analysis you want. The latest version of Comand Console can be downloaded from Affymetrix's website. We will only keep your data for three months, it is your own responsibility to make back up copies of the data you receive from us.
- All discounts, special wishes, planning, complaints, problems, etc... have to be discussed with and agreed by the lab-manager or they will not be considered valid.
More information? Questions?
Go to www.Affymetrix.com.
Contact the LGTC.
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