Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation

Jonathan Boxman, Naor Sagy, Sirisha Achanta, Rajanikanth Vadigepalli*, Iftach Nachman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Embryonic stem cells can spontaneously differentiate into cell types of all germ layers within embryoid bodies (EBs) in a highly variable manner. Whether there exists an intrinsic differentiation program common to all EBs is unknown. Here, we present a novel combination of high-throughput live two-photon imaging and gene expression profiling to study early differentiation dynamics spontaneously occurring within developing EBs. Onset timing of Brachyury-GFP was highly variable across EBs, while the spatial patterns as well as the dynamics of mesendodermal progression following onset were remarkably similar. We therefore defined a 'developmental clock' using the Brachyury-GFP signal onset timing. Mapping snapshot gene expression measurements to this clock revealed their temporal trends, indicating that loss of pluripotency, formation of primitive streak and mesodermal lineage progression are synchronized in EBs. Exogenous activation of Wnt or BMP signaling accelerated the intrinsic clock. CHIR down-regulated Wnt3, allowing insights into dependency mechanisms between canonical Wnt signaling and multiple genes. Our findings reveal a developmental clock characteristic of an early differentiation program common to all EBs, further establishing them as an in vitro developmental model.

Original languageEnglish
Article number31623
JournalScientific Reports
StatePublished - 17 Aug 2016


FundersFunder number
Seventh Framework Programme256495


    Dive into the research topics of 'Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation'. Together they form a unique fingerprint.

    Cite this