A continuous molecular atlas of reprogramming to iPSCs by high-throughput single cell RNA-seq
Jian Shu1,2,*, Marcin Tabaka1, Vidya Subramanian1, Justin Brumbaugh3, Konrad Hochedlinger3, Aviv Regev1, Rudolf Jaenisch2, Eric Lander1
1Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA; 2Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA; 3Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, Massachusetts, USA
Reprogramming somatic cells to iPSCs is a low efficiency process, with only a small fraction of cells capable of reaching pluripotency. Single cell RNA-seq can study the heterogeneity during reprogramming, however previous single cell RNA-seq analyses were based on gene expression profiles from limited genes or cells. Here we report a continuous high-resolution molecular reprogramming roadmap to iPSCs by analyzing approx. 70,000 single cells, with a computational analysis method developed to analyze this large scale dataset. Through progression analysis of each time points, it was discovered that early stage reprogramming is homogenous and that bifurcation begins after withdrawal of exogenous transcription factors. Cells that failed to become iPSCs expressed activation of certain lineage specification genes. Our data provides a high-resolution roadmap of reprogramming and the methods developed here can be used for future analysis of complex cellular programming and other reprogramming processes.