Analysis of RNAseq data Pinus sylvestris

Introduction:

Following the nuclear accidents in the Chernobyl (1986) and Fukushima Dai-Ichi (2011) nuclear power plants, vast areas of land were contaminated with radionuclides, leading to a long-term exposure of the environment to enhanced levels of ionising radiation. Pine trees such as the Scots pine (Pinus sylvestris, widespread throughout Europe), and the Japanese red pine (Pinus densiflora, an East Asian native), are particularly sensitive to radiation due to their large genome size and have hence been selected as a reference organism by the International Commission on Radiation Protection (ICRP, 2008). However, the mechanisms underlying their sensitivity are still largely unknown.

In the framework of his PhD Brix De Rouck has studied the responses of external gamma radiation on young pine seedlings (Pinus sylvestris, 0-10 weeks old) at different levels of biological complexity. To study the transcriptomic changes of genes in response to radiation an RNAseq was performed. Additionally, samples are still being processed for proteomic analysis at the MIC group. To finish his PhD Brix still needs to analyse the raw but big data sets and integrate them together with the already existing data in his PhD manuscript. As the data are presently at the SCK CEN server together with the programs and pipeline for the analysis, Brix needs to have access to the server and hence we would like to have this scientific volunteering position opened.

Objectives

• perform the analysis of the pine RNAseq data set obtained during the PhD
• perform the analysis of the proteomic data set when it becomes available
• integrate all data in the PhD manuscript with the already existing results papers
• Have regular update meetings with his mentors both for the analysis and pipelines as well as for the writing progress
• submit the thesis to the jury and schedule, have the internal defence, deliver the needed amendments if requested for and if possible also already prepare (and have) the public defence.
• submit the second paper and potentially 3rd paper