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Cell Rep DOI:10.1016/j.celrep.2020.108222

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.

Publication TypeJournal Article
Year of Publication2020
AuthorsKim, ISoo, Wu, J, Rahme, GJ, Battaglia, S, Dixit, A, Gaskell, E, Chen, H, Pinello, L, Bernstein, BE
JournalCell Rep
Date Published2020 Oct 06

Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) to embryoid bodies (EBs), a heterogeneous mixture of three germ layers. Here, we combine single-cell transcriptomics and genetic recording to characterize EB differentiation. We map transcriptional states along a time course and model cell fate trajectories and branchpoints as cells progress to distinct germ layers. To validate this inferential model, we propose an innovative inducible genetic recording technique that leverages recombination to generate cell-specific, timestamp barcodes in a narrow temporal window. We validate trajectory architecture and key branchpoints, including early specification of a primordial germ cell (PGC)-like lineage from preimplantation epiblast-like cells. We further identify a temporally defined role of DNA methylation in this PGC-epiblast decision. Our study provides a high-resolution lineage map for an organoid model of embryogenesis, insights into epigenetic determinants of fate specification, and a strategy for lineage mapping of rapid differentiation processes.


Alternate JournalCell Rep
PubMed ID33027665
PubMed Central IDPMC7646252
Grant ListDP1 CA216873 / CA / NCI NIH HHS / United States
R35 HG010717 / HG / NHGRI NIH HHS / United States
R01 HG009269 / HG / NHGRI NIH HHS / United States
F32 CA236432 / CA / NCI NIH HHS / United States
RM1 HG006193 / HG / NHGRI NIH HHS / United States