TTEST calculations help!

Hi there, I had generated a knockdown cell pool using shRNA against my target gene and control. i then subject these cells to the same conditions (DNA damage, etc).

I run experiments in triplicate usually, and then generate them independently 3 times.

i have some really basic questions, if you could help that would be great.

1. when i calculated standard deviation, i calculate the SD between the three means that I get from each independent experiment and not all 9 values from all experiments, correct?

2. in order to run a TTEST, do I use the three mean values from each independent experiment as my test array? or do I collate all my values i.e. 9 values per knockdown to calculate statistical significance (that is, if knockdown of target protein expression behaves differently to knockdown controls upon DNA damage, or other conditions).

3. Would this be considered a paired circumstance for t-test?

thanks! clueless with stats, and getting confused.