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Series GSE177051 Query DataSets for GSE177051
Status Public on Jan 27, 2022
Title Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Elucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. To overcome the limited scope and scalability of experimental methods in mapping this control, computational GRN reconstruction methods have been developed to infer relationships from transcriptomic data. We developed a new computational GRN reconstruction tool called Epoch, which takes advantage of single-cell RNA sequencing to address a number of shortcomings of existing tools including low precision, low sensitivity, and the limited ability to describe network topology changes over time. We used Epoch to identify the dynamic networks and key transcriptional regulators underpinning directed differentiation of mouse embryonic stem cells, and further demonstrate that modulating signaling pathways drives topological network changes that shape cell fate potential. By integrating signaling pathways with GRN structures, we traced how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively.
Overall design We perform single-cell RNA-sequencing on five time points spanning day 0 through day 4 of mouse embryonic stem cell day 0 through day 4 using the MULTI-seq protocol for sample multiplexing.
Contributor(s) Su EY, Spangler A, Cahan P
Citation(s) 35090587
Submission date Jun 11, 2021
Last update date Feb 23, 2022
Contact name Patrick Cahan
Organization name Johns Hopkins University School of Medicine
Department ICE and Biomedical Engineering
Lab Cahan Lab
Street address 733 North Broadway, MRB 653
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (1)
GSM5373540 d0d4_earlydiff
BioProject PRJNA736973
SRA SRP323746

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE177051_RAW.tar 88.0 Mb (http)(custom) TAR (of H5AD)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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