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Series GSE88927 Query DataSets for GSE88927
Status Public on Feb 06, 2018
Title Modeling signaling-dependent pluripotent cell states with boolean logic can predict cell fate transitions [II]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The process by which pluripotency is either maintained or destabilized to initiate specific developmental programs is poorly understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to combinations of input signals. While previous attempts to model PSC fate have been limited to static cell compositions, our approach enables simulations of dynamic heterogeneity by combining an Asynchronous Boolean Simulation (ABS) strategy with simulated single cell fate transitions using a Strongly Connected Components (SCCs). This computational framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) to simulate responses to LIF, Wnt/β-catenin, FGF/ERK, BMP4, and Activin A/Nodal pathway activation. For these input signals, our simulations exhibit strong predictive power for gene expression patterns, cell population composition, and nodes controlling cell fate transitions. The model predictions extend into early PSC differentiation, demonstrating, for example, that a Cdx2-high/Oct4-low state can be efficiently generated from mESCs residing in a naïve and signal-receptive state sustained by combinations of signaling activators and inhibitors.
Overall design Examination of perturbed PSCs versus control PSCs and mesoderm progenitors
Mouse pluripotent stem cells were grown on tissue culture plates for two days in serum-containing, feeder free medium supplemented with the following cytokines/small molecules:
2i = CHIR99021 (Reagents Direct 27-H76 – 3µM) & PD0325901 (Reagents Direct 39-C68 – 1µM)
Jaki = JAK inhibitor (EMD Millipore 420097 – 2.0µM)
BMP = BMP4 (R&D Systems 314-BP-010 – 10ng/ml)
Alk5i = ALK5 inhibitor II (Cedarlane ALX-270-445 - 10µM)
Contributor(s) Yachie-Kinoshita A, Onishi K, Ostblom JE, Posfai E, Rossant J, Zandstra PW
Citation(s) 29378814
Submission date Oct 19, 2016
Last update date May 15, 2019
Contact name Peter Zandstra
Organization name University of Toronto
Department Institute of Biomaterials and Biomedical Engineering
Street address 160 College Street, University of Toronto
City Toronto
State/province Ontario
ZIP/Postal code M5S 3E1
Country Canada
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (8)
GSM2355302 mesoderm-progenitor-day3 (II)
GSM2355303 mesoderm-progenitor-day4 (II)
GSM2355304 CDX2-GFP-positive-sorted-ESCs-from-2i-Jaki-BMP-Alk5i-day2 (II)
This SubSeries is part of SuperSeries:
GSE88928 Modeling signaling-dependent pluripotent cell states with boolean logic can predict cell fate transitions
BioProject PRJNA349134
SRA SRP091764

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Supplementary file Size Download File type/resource
GSE88927_RAW.tar 1.8 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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