generally we use multiple shRNA's for a gene knock down, but often i observed that although few of the shRNA's target the same ORF region or UTR, their outcome is different, why this is so??
Moreover The same shRNA working in one cell line does not wok in other cell line, why it happens?
Also sometimes the shRNA that does not give you best knock down (in comparison to other clones) gives you best knock down phenotype, why it happens??
When you create stable knocked-down cell lines with shRNA, the plasmid (containing the sequence for producing shRNA) that you infected will be insert randomly in the genome of the cell. This can alter the gene expression of other gene and at the end can alter the proteome of the cells. That's why you can have different outcomes with different shRNA and in different cell lines
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