Sequencing
Sequencing and automation technology
Overview
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Recently three new DNA sequencers have been announced, that are able to analyse DNA sequences with an unprecedented productivity: the FLX (Roche-454 Life Sciences), the Solexa (Illumina) and the SOLiD (Applied Biosystems) systems. Currently we are completing some preliminary analysis carried out with the three different systems, in particular we have acquired newly the SOLiD Technology and we are planning applications in metagenomics, transcriptomics and human disease for the future development of our projects. To learn more about SOLiD Technology visit Applied Biosystems dedicated section. | 
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Team
Our Sequencing Team is direct by Riccardo Schiavon as team leader of SOLiD System, Michela D'Angelo e Rosanna Zimbello as coordinators of SOLiD sequencing.
Resources
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Our technology resources include:
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Some Applications
Tomato project future strategy
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Whole genome shotgun (WGS) sequencing by means of 454 GS FLX Titanium (Roche). Next generation sequencers, such as 454-Roche, have increased the volume of sequencing conducted by the scientific community and expanded the range of problems that can be addressed by the direct readouts of DNA sequence. Of the three massively parallel DNA sequencing platforms already commercialized, only the 454 platform (Roche) has been designed to allow a de novo sequencing approach, which will be required by the Nannochloropsis genome project (Miller et al. 2008). | 
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The genome sequencing will be performed by means of two different 454 FLX Titanium runs: one of long single pass reads (average length around 400bases) and the other of long-paired end reads, that assures up to 20kb physical distance between the two ends. Although for technical reasons the latter run will give less sequence coverage, it will produce an extremely high physical coverage of the genome, that is important for obtaining a good assembly that will produce an accurate scaffold of the entire genome, where most of the contigs should be incorporate in a reasonable number of super-contigs.
Grape Genome project past and future
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We sequenced the grape genome by developing a system for high throughput sequencing for preparing large-scale plates of DNA, from the amplification stage to the pre-purification before sequencing stage, using a series of automatic robot-pipettes of last generation for preparation plates of DNA from 384 wells and then loaded in three DNA Analyzer 3730 XL used at full pace in this project. The data collected in a database were analyzed and subjected to NCBI. | 
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For the future firstly, we want to apply some "new generation" sequencing technologies to analyse the expression pattern in a few different tissues and varieties of Grape. The FLX (Roche-454 Life Sciences), is able to produce up to 80-100 million bases per run, as single sequences of about 200 bases, the Solexa (Illumina) and the SOLiD (Applied Biosystems) systems can produce up to one billion bases per run, but they produce shorter sequences of 30-35 bases. These analyses will be performed mainly at the cDNA level. Some pilot experiments have been carried out as a part of the main Grape Genome Project, with the three different systems and are now almost completed. The objective of this new project is to extend those pilot experiments to have a more complete picture of the transcriptome and to identify polymorphic sites.
Laboratory Automation
Our laboratory of sequencing and automation has developed an high throughput system aimed to preparation, extraction and sequencing of DNA, applicable to genome sequencing. We are setting a procedure of automation in developing, integrating various steps of the process until the final phase of sequencing. Through the use of automatic multidispencers, thermal cyclers and centrifuges of last generation, we are studying a coordination, which represents the future of the preparation of samples, applicable to large scale genome sequencing.
We have people who are developing a series of formalized protocols to be applied to a management system Laboratory automation.