Why not use datasets already available?

I have been asked why I don't use the data that's already available? 

Short answer: the RNA sequence data available isn't very rich.

Most of the datasets have constructed single end libraries so fragments of messages are only being read from one side for very short reads. This means that if there are any splice variants of transcripts they will not be picked up. In mammals and plants splice variants or isoforms have been attributed to large changes in the cell. In filamentous fungi, while there have been evidence of isoforms the effect they have on cellular control has not been well investigated. 

Since the transition into dormancy from a vegetative state is a major growth phase process I believe the spore will contain a number of splice variants which play a crucial role in regulating dormancy. I have constructed pair end libraries with large fragments so I can detect variants.

Secondly, the sequencing reads have been very shallow. Which means if I was looking for top genes with lots of transcripts then it would be easy to pick up. Most of these "critical" genes have already been picked and analyzed. However, there are genes that are not highly expressed which have a huge impact on the cell especially when it comes to shifting growth phases. It is also the combined action of lowly expressed genes that can have high impact, for instance in secondary metabolite pathways. Secondary metabolites such as melanin production or the way the cell wall is "decorated" has shown to help spores resist environmental stress and "detect" it's environment while in a dormant state.

Lastly, most of the transcriptome datasets available are based on a less pathogenic, more environmental strain of Aspergillus fumigatus. I have built my library using the more pathogenic clinical strain so that I can compare spores between highly pathogenic clinical strain and less pathogenic environmental strain thus giving us a better insight as to what genes inside the spore are responsible for heightened virulence. 

In conclusion, the transcriptome dataset that I am proposing to generate would be not like any other dataset we have for Aspergillus fumigatus spores. It will provide a deep knowledge of how stress conditions can impact how messages are packaged into the spore and if there are gene variants that we have not credited to the regulation in spore dormancy and germination.