Hello, Here is lot of about RNA-Seq time course experiments so I have chaos. If is somewhere correct answer for me, please send me link.
I have time course experiment - 3 condition - 1 control + 2 treated, and 4 times
LibraryName countf condition time 1 WT-0-mpw-B WT-0-mpw-B_union.count WT 0 2 WT-0-mpw-D WT-0-mpw-D_union.count WT 0 3 WT-30-mpw-A WT-30-mpw-A_union.count WT 30 4 WT-30-mpw-D WT-30-mpw-D_union.count WT 30 5 WT-60-mpw-C WT-60-mpw-C_union.count WT 60 6 WT-60-mpw-D WT-60-mpw-D_union.count WT 60 7 WT-90-mpw-B WT-90-mpw-B_union.count WT 90 8 WT-90-mpw-D WT-90-mpw-D_union.count WT 90 9 TRIM-0-mpw-A TRIM-0-mpw-A_union.count TRIM 0 10 TRIM-0-mpw-B TRIM-0-mpw-B_union.count TRIM 0 11 TRIM-30-.... TRIM-30-mpw-A_union.count TRIM 30 12 TRIM-30-.... TRIM-30-mpw-B_union.count TRIM 30 13 TRIM-60-.... TRIM-60-mpw-A_union.count TRIM 60 14 TRIM-60-.... TRIM-60-mpw-B_union.count TRIM 60 15 TRIM-90-.... TRIM-90-mpw-A_union.count TRIM 90 16 TRIM-90-.... TRIM-90-mpw-B_union.count TRIM 90 17 enNOS-0-.... enNOS-0-mpw-A_union.count enNOS 0 18 enNOS-0-.... enNOS-0-mpw-D_union.count enNOS 0 19 enNOS-30.... enNOS-30-mpw-B_union.count enNOS 30 20 enNOS-30.... enNOS-30-mpw-D_union.count enNOS 30 21 enNOS-60.... enNOS-60-mpw-C_union.count enNOS 60 22 enNOS-60.... enNOS-60-mpw-D_union.count enNOS 60 23 enNOS-90.... enNOS-90-mpw-A_union.count enNOS 90 24 enNOS-90.... enNOS-90-mpw-C_union.count enNOS 90
I want compare changes in gene expression during time (I don't care about differences at time 0). What is correct design for DESeq2 to find theese genes?
(For example - 1 gene in control have maximum expression at time 30 and after that, expression rapidly decrease, but in treated samples expression of theese gene is still increased. But at the time 0 - in sample TRIM expression level is simillar with WT and in sample enNOS is increased.)
Thanks.