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Updated: Jan 26, 2026

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
Published on: January 7, 2020
Ultra-multiplexed analysis of single-cell dynamics reveals logic rules in differentiation
Ce Zhang1,2,3, Hsiung-Lin Tu1,2,4, Gengjie Jia2
1Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
Abstract:
Dynamical control of cellular microenvironments is highly desirable to study complex processes such as stem cell differentiation and immune signaling. We present an ultra-multiplexed microfluidic system for high-throughput single-cell analysis in precisely defined dynamic signaling environments. Our system delivers combinatorial and time-varying signals to 1500 independently programmable culture chambers in week-long live-cell experiments by performing nearly 106 pipetting steps, where single cells, two-dimensional (2D) populations, or 3D neurospheres are chemically stimulated and tracked. Using our system and statistical analysis, we investigated the signaling landscape of neural stem cell differentiation and discovered "cellular logic rules" that revealed the critical role of signal timing and sequence in cell fate decisions. We find synergistic and antagonistic signal interactions and show that differentiation pathways are highly redundant. Our system allows dissection of hidden aspects of cellular dynamics and enables accelerated biological discovery.
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