An experimental sample is a group that receives the variable being
tested in an experiment. The control group is the group in an
experiment that does not receive the variable you are testing using
the same experimental procedure. Therefore the control group,
receiving no intervention, is used as a baseline to compare groups and assess the effect of that intervention.
I gave this as an object lesson to show that test and control must be linked by a similar experimental procedure. So yes, if you were to normalize then use the entire matrix.
Additional point (bonus round)
The purpose of data transformations is to make data easier to model and understand. One purpose of transforming data is to find outliers, reduce the amount of skew, etc.
Looking at a small part of your data, it seems like the values are between 0-100, Suggesting that normalization is not entirely necessary, IMHO.