Which kit, the QIAprep 96 Plus Miniprep Kit or the QIAGEN Plasmid Plus 96 Miniprep Kit, do you recommend for transfection?

For sensitive cell lines and downstream assays, we recommend QIAGEN Plasmid Plus 96 Miniprep Kit, because the endotoxin value is below 1 EU/µg DNA.  The QIAGEN Plasmid Plus 96 MiniPrep kit contains a special protocol for endotoxin removal.  Combination of other chemistries (such as Buffer ER) is not possible with this kit.  For robust cell lines, the QIAprep 96 Plus Miniprep Kit may be okay, as the endotoxin values are below 10 EU/µg DNA.