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Illumina BeadChips
System
The Leiden Genome Technology Center has a complete Illumina BeadArray system including a BeadStation500GX with autoloader, a Tecan EVO robot, hybridization ovens and all the necessary equipment to perform Illumina Sentrix BeadChip and Sentrix Array Matrix (SAM) hybridizations and scanning, and data analysis.
Arrays and assays
- DNA
- whole-genome SNP genotyping and CNV analysis - Infinum assay
- focused content - Infinium and GoldenGate assay
- linkage - Infinium and GoldenGate assay
- RNA
- whole-genome SNP genotyping and CNV analysis - Infinum assay
- focused content - Infinium and GoldenGate assay
- Methylation profiling
- Protein analysis
See the Illumina website for more information on the Illumina BeadXpress and the VeraCode technology, assays and types of beads, custom and standard.
Illumina at the LGTC
Projects
When you have a project for Illumina BeadArrays and have not used the system before it is necessary to discuss it with the LGTC. We can help you discuss and evaluate the possibilities, costs, planning, and all other issues. For large projects or series of samples of bad sample quality it may be wise to start with a pilot experiment. For large amounts of samples we offer the possibility that you do the hybridizations and scanning yourself.
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 Illumina BeadArray experiments contains the following products: Illumina order charge, BeadChips or SAM (includes all reagents for hybridization), optional: kit for the labeling of the RNA (RNA projects only), hybridization of the BeadChips either done by the LGTC or by yourself. 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. If you do the hybridization yourself you need to be trained on the system by a LGTC technician and will need to make a separate appointment for the laboratory training.
Labeling of RNA samples
For expression analysis: prepare your RNA, double strand cDNA, and biotin-labeled cRNA. To perform this labeling procedure, use the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion catalog #AMIL1791). This kit can be ordered via the LGTC. We do not offer services for the labeling on a regular basis, but there is always an option to discuss the possibilities.
Sample delivery
Once you are ready to deliver your samples (DNA or labeled cRNA) you need to complete this Illumina sample sheet and mail it to info@lgtc.nl mentioning "Illumina sample sheet" in the subject. Without a quotation or sample sheet we will not start processing your samples and we will not train you on the system. In the Illumina sample sheet you will find the minimal volumes and concentration needed and requested for the Illumina assays.
Planning and time span
According to our terms and conditions, results will be delivered four weeks after the delivery of the samples, when delivered in the right volumes and concentrations. 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.
When doing the hybridizations yourself, once you have been trained on the system by a LGTC technician, the planning is up to you. Book your time in the Illumina Yahoo calendar.
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, or you can download it from the network for larger projects. When you do the scanning yourself you need to copy your data to an external hard drive. In all the cases: we will not keep your data for longer than three months, it is your responsibility to make your own back ups.
The LGTC has a data-analysis PC available for Illumina BeadArray users with Illumina's latest version of GenomeStudio installed. You need to be authorized to get access to this computer, there is also a Yahoo calendar available to make reservations.
Summary: what can you expect from us? General rules
- Hybridization of samples, either do it yourself or via the LGTC:
- The LGTC will do the hybridizations when included in your quotation. We will do the hybridizations according to Illumina BeadArrays latest protocols. When the run has failed, the LGTC cannot be held responsible and the issue will be discussed with you. BeadChips or SAMs will not be refunded and not re-run for free.
- When you do the hybridizations yourself it is your responsibility to follow the protocols described by Illumina. When in doubt ask the LGTC. The LGTC is not responsible for any failed runs due to any reasons.
- You will receive the raw data either on DVD or via a network drive. When scanning yourself 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 GenomeStudio is available on a LGTC computer and free to use. 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.illumina.com.
Contact the LGTC.
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