I am currently doing an RNA-seq study that deals with the effects of a toxic compound.
It is not very surprising to me, but most genes are up regulated when the organism (insect) is exposed to the toxic compound. What can people say having more experience with this? Is this the general picture.
I am looking for a review/paper that deals with this to read more. Do you have a good suggestion?
EDIT, some more information:
We study the effects of a toxic compound on insects.
We have Illumina-sequenced the Transcriptome of: 5 biol. Replicates for Control, 5 biol. Replicates for 1x concentration of the compound and 5 biol. Replicates for 10x concentration of the toxic compound.
First I did a Trinity-assembly using all 15 biol. replicates. Then I map the the data back to the assembly using bowtie2 and then use RSEM. After that I use Trinity scripts to calculate DE (using EdgeR) and to output the significantly DE genes.
For both conditions, I see mostly up regulated genes. For the 1x concentration about 60 (50 up regulated), for the 10x concentration about 280 (230 up regulated). This makes sense, the number of of diff. regulated genes correlates with the concentration of the toxic substance.
If we check the overlap between the DE genes of the two treatments, I have about 25 DE genes. Those are ALL up regulated.
So, would you say that this compound mainly up regulates genes or could this be an artefact of the de novo-based method?