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Series GSE93301 Query DataSets for GSE93301
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
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.
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.
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
Street address Einsteinweg 55
City Leiden
ZIP/Postal code 2333CC
Country Netherlands
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (11)
GSM2450576 0h-rep1
GSM2450577 0h-rep2
GSM2450578 06h
BioProject PRJNA360574
SRA SRP096320

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Supplementary file Size Download File type/resource
GSE93301_CDS_3UTR_counts.txt.gz 503.6 Kb (ftp)(http) TXT
GSE93301_RAW.tar 10.2 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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