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| Status |
Public on Apr 25, 2023 |
| Title |
Integration of a multi-omics stem cell differentiation dataset using a dynamical model |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.
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| Overall design |
mRNA profiles of mouse embryonic stem cells (E14) during retinoic acid mediated differentiation. Samples were collected at 0h (duplicate), 6h, 24h, 36h, 48h, 72h and 96h (duplicate). Additionally, 2 samples were collected at 96h after sorting cells into extra-embryonic endoderm-like (XEN) and ectoderm-like (ECT) fractions.
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| Contributor(s) |
van den Berg PR, Slavov N, Semrau S |
| Citation(s) |
37167320 |
| |
| Submission date |
Jan 09, 2017 |
| Last update date |
Jul 28, 2023 |
| Contact name |
Stefan Semrau |
| Organization name |
Leiden University
|
| Department |
Physics
|
| Lab |
Quantitative Single Cell Biology
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| Street address |
Einsteinweg 55
|
| City |
Leiden |
| ZIP/Postal code |
2333CC |
| Country |
Netherlands |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA360574 |
| SRA |
SRP096320 |
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