PTPome-wide functional RNA interference screening methods

The elucidation of the entire complement of genes encoding protein tyrosine phosphatases (PTPs) in human genome, the human ‘PTPome’, has made it possible to experimentally address the entire family in an unbiased manner. Here we describe a functional RNA interference-based assay, in which we evaluate 87 of the known 107 PTPs for effects on cell survival in a high throughput manner. The details of assay rationale and design, instrumentation, pitfalls, data analysis, and further validation steps are described. We also discuss the suitability of this technology for further assay development and application to other functional read-outs and signaling pathways.