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Helicos Next generation Sequencing (Helicos NGS)
Systems
The Leiden Genome Technology Center has a Helicos Genetic Analysis System, including a Heliscope Single Moecule Sequencer (HSMS), a HeliScope analysis engine and two Heliscope sample loaders.
Technology
More information on the sequencing by synthesis technology on the HSMS can be found on the Helicos website or on the Helicos specification sheet.
Applications
- Current Applications:
- Targeted Resequencing
- Whole Genome Resequencing
- Digital Gene Expression
- ChIP-seq
- Helicos DNA Barcoding
- Future applications:
- Digital Copy Number Variation (CNV) Analysis
- Small RNAs, including microRNA
- Whole Transcriptome Sequencing
- Epigenetics - Methylation
- Allelic imbalance
- Genomic rearrangements
- Paraffin-embedded tissue DNA
Helicos NGS at the LGTC
Projects
When you have a project for Helicos NGS it is necessary to discuss it with the LGTC. We can help you discuss the possibilities, costs, planning, and all other issues. For most of the projects it is wise to start with a pilot experiment. We will also advise you to do the sample preparation yourself under supervision of the LGTC.
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 Helicos NGS contains the following products: sample preparation reagents, sample loading, sequencing, Helicos NGS support, and initial alignment of data. We do not do data analysis on a regular basis, if you want the LGTC to do the data analysis, it has to be included in the quotation. 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.
Samples
Once you are ready to deliver your samples you need to complete this Helicos Next generation sample sheet and and mail it to info@lgtc.nl mentioning "Helicos NGS sample sheet" in the subject. Without a quotation or sample sheet we will not start processing your samples. When you do the sample preparation yourself, the protocol you are using has to be approved by Helicos or by the LGTC. Wrong sample preps will give bad sequencing results. Once you are finished with the samples you will need to do a lab-on-a-chip and send the files with the measured molarity. We will check the data before we start the sequencing. You need to be absolutely sure of the molarity of your samples; wrong concentrations will give problems and give bad sequencing results.
Planning and time span
According to our terms & conditions, results will be delivered within three months after the start of the project. For exeptional projects we may need more time. If that is the case for your project it will be mentioned in your quotation. The project starts when the samples are delivered to the LGTC together with the signed quotation and the sample sheet. When unexpected circumstances occur that delays the planning, you will be notified.
Data and data analysis
The quotation does not automatically include data analysis since the LGTC will not do the data analysis of your samples. If you want complete data analysis to be done it has to be included in your quotation. On the internet and via courses you can get all the information you need for Helicos NGS data analysis. We will only do the basic QC, base calling, and initial zipping of the data. From that point you will receive the data from us. You will be able to download it via a FTP server. The files you receive are FASTQ and SRF files with the sequencing data and quality values of the called bases. With these files you can do the data analysis, for more information see NGS Bioinformatics.
Summary: what can you expect from us? General rules
- The LGTC will do the sample loading and the sequencing. When the run has failed due to technical problems with the Helicos or the sample loading we will re-run your samples for free. All other causes of failed runs will not be refunded and not re-run for free.
- You will receive FASTQ and SRF files (includes sequences and quality values of the base calling). 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 other wishes concerning the data will be considered as data analysis for which you will receive a separate quotation.
- 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.helicosbio.com.
Contact the LGTC.
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