I am a computer engineering student currently doing a research about the Trinity platform. I've chosen arabidopsis thaliana as my model organism. I downloaded small sets of data from SRA to test, but I need a large amout of raw data for my purpose. From where can I download all the raw transcriptome data for the species as a whole? 
You could try an Entrez query like http://www.ncbi.nlm.nih.gov/sra?term=((Arabidopsis%20thaliana%5BOrganism%5D)%20AND%20%22biomol%20rna%22%5BProperties%5D)%20AND%20%22study%20type%20transcriptome%20analysis%22%5BProperties%5D . This produces a list of almost 5000 Arabidopsis transcriptomes accessions. On the top of your Entrez result page you can send the results to the "Run Selector" and then download the list of all Arabidopsis transcriptomes accessions and feed that into the SRA toolkit. It looks like about 6 Tb of data in all.