I am doing RNA-seq analysis of DE genes from mare's endometrial biopsies. We collected our samples at an abattoir due to restrictions with samples collected from live horses.
Thus, I have three time points: alive_0h (when the mare was just slaughtered, tissue representing the uterus of a live mare still). Then we took biopsies from the uterus and used them in a tissue culture. After culturing the explants we had 2 time points (24h and 48h) for both control and LPS challenge.
I am having a hard time trying to figure out the design I should use since I have this samples at 0h. We have 5 biological replicates (horses).
My LRT design is the following one:
ddsLRT_exp3 <- DESeqDataSet(se_exp3, design = ~ horse + treatment)
ddsLRT_exp3 <- estimateSizeFactors(ddsLRT_exp3)
ddsLRT_exp3 <- estimateDispersions(ddsLRT_exp3)
ddsLRT_exp3 <- nbinomLRT(ddsLRT_exp3, reduced = ~ horse)
resLRT_exp3 <- results(ddsLRT_exp3)
My colData is:
Our aims are to compare:
1) Control vs LPS at 24h and 48h
2) LPS 24h vs 48h
3) Alive 0h vs Control 24h vs Control 48h
Many thanks indeed!