I have got transcriptome gene sequencing of 6 groups as mentioned follow.

Group 2 days (Control vs Treatment)

Group 10 days (Control vs Treatment)

Group 15 days (Control vs Treatment)

I have got 290 DEGs.

49 down/up present in group 2 days

100 down/up present in group 10 days

139 down/up present in group 15 days

I select 20 genes for qPCR .

Mistakenly i select those which are not present in all 3 groups.

Some of them are in group "2 days" some are in "10 days" and some are in "15 days".

Only 2 are same in 2 days and 10 days.

I have also done immunohistochemistry for 2 genes.

Now my question is that, is it possible in same model, sampling done on 2 days and then 10 days. Does the genes change? Not the expression changes but the gene does not differentially expressed.

If the gene does not expressed at 2 days and then expressed (up or down) on 10 days. How to deal with this ?

The big problem is that, Mostly the problem is that genes are not express on 2 days or 10 days but they are expressed on 15 days and genes are down regulated.

How to deal with this? is this reliable data? can we publish?