I'm beginning a RNAseq analysis looking for genes that vary in expression across a thermal gradient (12 temperature points) in a non-model (no genome) organism. My data consists of Illumina 100bp PE data for 12 temperature points. Basically, what I'd like to get is the reaction norm for each gene in the transcriptome. This seems like a straight-forward approach to me, but my searching of the literature has not turned up any studies that have done this(!?). To my understanding, the standard methods for gene expression analysis (DeSEQ) only work for pair-wise or multi-factor designs, not a regression design as I've proposed. The closest I've found is this article Abundant gene-by-environment interactions in gene expression reaction norms to copper within Sacharomyces cerevisiae, but this paper uses spotted microarrays (I have Illumina) and thus performs pair-wise comparisons.
I have plans on how to go about this analysis, but am interested in suggestions from the Biostars community or recommendations of citations I may have missed.
Thanks for any suggestions in advance, John