The discovery of the human genome has unveiled new fields of genomics,
transcriptomics, and proteomics, which has produced paradigm shifts on how
to study disease mechanisms, wherein a current central focus is the under-
standing of how gene signatures and gene networks interact within cells. These
gene function studies require manipulating genes either through activation or
inhibition, which can be achieved by temporarily permeabilizing the cell
membrane through transfection to deliver cDNA or RNAi. An efficient trans-
fection technique is electroporation, which applies an optimized electric pulse
to permeabilize the cells of interest. When the molecules are applied on top of
seeded cells, it is called “direct” transfection and when the nucleic acids are
printed on the substrate and the cells are seeded on top of them, it is termed
“reverse” transfection. Direct transfection has been successfully applied in pre-
vious studies, whereas reverse transfection has recently gained more attention
in the context of high-throughput experiments. Despite the emerging impor-
tance, studies comparing the efficiency of the two methods are lacking. In this
study, a model for electroporation of cells in situ is developed to address this
deficiency. The results indicate that reverse transfection is less efficient than
direct transfection. However, the model also predicts that by increasing the
concentration of deliverable molecules by a factor of 2 or increasing the
applied voltage by 20%, reverse transfection can be approximately as efficient
as direct transfection.