Optimized reporters for multiplexed detection of transcription factor activity

A library of 35,500 reporters was designed for 86 TFs in order to identify optimized TF reporters. The library was transfected into diverse cell types and probed upon almost 100 TF perturbations. To compare TF activities with TF abundances, RNA-seq data was used. For mNPCs, mESCs and HepG2 cells, RNA-seq data was generated in house. For thee TF knockdowns in HepG2 cells, RNA-seq data was generated to validate the experimental design. We quantified gene expression levels by RNA-seq in mNPCs derived from ES-E14tg2a (Peric-Hupkes et al., PMID: 20513434), ES-E14tg2a cells, and HepG2 cells. 1x10^6 cells were cultured and subjected to RNA-seq in two to three biological replicates.