TF-seq: A systematic characterization of transcription factor reprogramming effects at single-cell resolution

A systematic single-cell quantitative screen involving TF overexpression is essential to comprehend the programming effects of numerous TFs in the context of networks, as well as the reprogramming heterogeneity and its molecular basis. Here, we developed TF-seq, aligning doxycycline-inducible barcoded ORF overexpression of individual TFs with transcriptomic changes captured by scRNA-seq, to map the programming properties of each TF at single-cell resolution. We conducted TF-seq on mouse embryonic mesenchymal stem cells for 435 mouse TFs in parallel, which created a dataset consisting of both the transcriptome and TF overexpression levels for ~52,000 cells. Specifically, the quantification of the TF dosage revealed heterogeneous cellular and molecular responses and novel capacities of known TFs and uncharacterized TFs. Our TF library, single-cell TF gain-of-function atlas, and analytic frameworks can serve as valuable resources and references for a mechanistic understanding of the roles of TFs in governing cell states. For analysis and more details about this data, you can check our GitHub: https://github.com/DeplanckeLab/TF-seq