Deep Sequencing

Werner Van Belle¹^* - werner@yellowcouch.org, werner.van.belle@gmail.com
Ina Nissen¹ - ina.nissen@bsse.ethz.ch
Michael Stadler² - michael.stadler@fmi.ch
Christian Beisel¹ - christian.beisel@bsse.ethz.ch

1- Deep Sequencing Unit Department of Biosystems Science and Engineering ETH Zurich; Mattenstrasse 24, Building 1058, Basel; Switzerland
2- Friedrich Miescher Institute; Mattenstrasse 28, Basel; Switzerland
* Corresponding author

Abstract : In parallel to the human genome sequencing initiative several new technologies have emerged that allow sequencing at unprecedented throughput and low costs. These approaches are generally referred to as “deep sequencing”. They enable researchers to not only re-sequence genomes and thus to identify genome variations but also to quantify the abundance of experimentally enriched fractions of the genome. The very large numbers of short individual sequence reads produced by the Illumina Genome Analyzer (currently approx. 50 million reads per instrument run) are well suited to make direct quantitative measurements of the sequence content of a DNA sample. By determining a short sequence read from each of many randomly selected molecules from the sample and then mapping each sequence read onto the reference genome, the identity of each starting molecule is learned, and its frequency in the sample can be calculated. Desired levels of sensitivity and statistical certainty, needed to detect rare molecular species, can be achieved by adjusting the total number of sequence reads. Sequence census assays do not require knowing in advance that a sequence is of interest as a promoter, enhancer or RNA-coding domain, as most current microarray designs do. The combination of chromatin immunoprecipitation assays with the subsequent quantitative analysis of the enriched DNA sample by deep sequencing (ChIP-seq) has been proven to be of great value for whole mammalian genome approaches in several high-profile studies published over the last year. At D-BSSE we have established a deep sequencing unit based on Illumina sequencing technology located in the new “Laboratory for Quantitative Genomics”. This poster gives an overview of the sequencing technology and the data analysis pipeline. Furthermore it provides insights into the quality of our functional genomics data recently generated by ChIP-seq and RNA-seq.

Keywords: deep sequencing, sequencing by synthesis, CHIP-SEQ
Reference: Werner Van Belle, Ina Nissen, Michael Stadler, Christian Beisel; Deep Sequencing; Presented at All Systems X day; Switzerland; October 2008
Files: SystemsX.pdf
See also:
The research article.
The browsable correlation maps between Histone Methylation and Acetylation tracks
Some posters [1, 2, 3]
Presentations of this research at FMI, Novartis, UNIL, University Zürich and ETH Zürich [1, 2]

http://werner.yellowcouch.org/
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