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| Status |
Public on Nov 11, 2022 |
| Title |
Expression data from MCF10A cells treated with TGFβ for multiple time points [miRNA-4] |
| Platform organism |
synthetic construct |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
We combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. Here we apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; –unexpected topological coupling between omics, –four distinct cell states during EMT (E, E/M-1, E/M-2, M), –omics-specific kinetic paths, –stage-specific multi-omics characteristics, –distinct regulatory classes of genes, –ligand–receptor mediated intercellular crosstalk using an innovative pipeline integrating scRNAseq and subcellular proteomics, and –novel combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, while this study provides an unprecedented resource on TGFβ signaling and EMT, PAMAF-like workflows can be applied to generate comprehensive molecular landscapes of other multifaceted biological processes.
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| Overall design |
MCF10A cells treated with TGFβ for multiple time points
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| Contributor(s) |
Paul I, Emili A |
| Citation(s) |
36755019 |
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| Submission date |
Jan 19, 2022 |
| Last update date |
Mar 02, 2023 |
| Contact name |
Andrew Emili |
| E-mail(s) |
aemili@bu.edu
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| Organization name |
Boston University
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| Department |
Biochemistry
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| Lab |
CNSB
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| Street address |
72 East Concord St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
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| Platforms (1) |
| GPL19117 |
[miRNA-4] Affymetrix Multispecies miRNA-4 Array |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE194019 |
Expression data from MCF10A cells treated with TGFβ for multiple time points |
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| Relations |
| BioProject |
PRJNA798732 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE194008_RAW.tar |
6.8 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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