I am currently working with the technical team at ACD Biosystems to resolve some background staining that I observe when using their fluorescent multiplex kit (http://www.acdbio.com/rnascope%C2%AE-multiplex-fluorescent-assay). I am hoping this method will allow me to measure knockdown of an shRNA-targeted mRNA. Unfortunately, the positive and negative controls are showing some background staining that is nonspecific. I would like to know if anyone else has worked with the RNA Scope protocol and could provide input on how things worked out for you. Thanks!
http://www.acdbio.com/rnascope%C2%AE-multiplex-fluorescent-assay