We have an experimental design as seen below
Where we administered drug at 0 min for each mouse genotype and took them down at given below intervals. wt and ko mouse models were administered only with the vehicle which would be our negative control.
Performed rnaseq (total rna) truseq stranded protocol would like to see differences between each time point compared to the vehicle, used star aligner to align to mm9 , htseq for gene counts .
sample type time WT Vehicle 30 min KO Vehicle 30 min WT Drug 30min KO Drug 30min WT Drug 1 hour KO Drug 1 hour WT Drug 2 hour KO Drug 2hour WT Drug 3 hour KO Drug 3hour
We do not have any replicates and hence cannot use any of the differential expression statistical tools (asked this question at bioconductor where Dr. Love himself replied link to question asked) where he suggested a linear model.
we were wondering if someone could help us with any such design (papers/previously performed analysis) what we would like to see is comparison/differences (significant) between these groups (veh vs 30min, veh vs 1 hour, beh vs 2 hours, veh vs 3 hours)