Transcriptome analysis via 454 sequencing
In vitro veritas
Several improvements in DNA sequencing technology were made in the last few years, after several decades of Sanger sequencing domination. A prominent technology, delivered by Roche, is the 454 FLX sequenator, that exploits emulsion PCR and pyrosequencing to provide an extremely fast DNA to sequence pipeline. Current model can provide up to 100.000.000 bases per run, that takes approximately 7 hours and a half. The downside of this new technology is that the 900 bases long reads of the optimized Sanger method dropped to 350.
I'd like to investigate transcriptomes with this new device, that represent a high throughput approac for 5'-CAGE, alternative splicing discovery and genome annotation with EST library sequencing.
High pressure adaptation of P. profundum
a microarray based platform
For my master degree I worked on a project aiming to decipher P. profundum SS9 transcriptome, its changes in high pressure adaptation, and the role of a transcription factor (ToxR) in this adaptation. In particular, comparing the transcriptional landscape of the wild type strain and a ToxR-defective strain, we were able to obtain a list of putative ToxR-regulated transcripts.
The technique we used was a custom microarray from CombiMatrix. This was the first project at the University of Padua that made use of it, and a notable part of my work was the set up of procedures and the development of bioinformatics tools to support this new pipeline.
Highlights
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