I have retrieved different datasets (supplementary raw data as well as in SRA format) from GEO, NCBI related to particular virus. I am interested to study the differential gene expression and further downstream analysis relating with various celllular pathways. I have also retrieved the data related to miRNA. Now before performing analysis of selected datasets there are few doubt which I am not sure about.One more thing is that I will take help from my collaborator for analysis because I am new to this kind of work. But I have to set the objective for the analysis work. So I need help for setting objective here I mean what are the possibilities of analyzing retrieved data. Should I focuss on supplementary file and select some of the genes from there or start a fresh analysis again. Do I will get anything new when I will align again to same reference genome or some other (other virus strain are available). In short what can be the proper experimental design for analyzing already analyzed data after retrieving from GEO. Please excuse me if questions does not look ordered and looks fragmented, I am new to this.
Looking forward for the suggestions and possible answers thanks in advance