Paired vs unpaired t test

#1
Hi,

Following is my experimental condition -

I have chronically treated normal cell line with smoke condensate for 12 months. Over the time the cells have changed their morphology and characteristic. They have transformed into cancerous cells - the cells morphology has changes (shape/size), they have gained all the characteristic of cancerous cells. To characterize the changes I have carried out genomic and proteomics analysis. But I am confused now - whether to use paired or unpaired t test to compare the parental with cancerous form of the cells. Could you please tell me whether to use paired or unpaired analysis. I am inclined towards unpaired as over the continuous exposure of cells to smoke for 12 months the characteristic properties (which define cells as normal/cancerous) have changed.

Thank you for your time.
 
#2
When you use dependent samples you use paired t. For example you compare the same person before treatment and after treatment. Can you paste some data for better understanding?