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Series GSE194008 Query DataSets for GSE194008
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
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.
Overall design MCF10A cells treated with TGFβ for multiple time points
Contributor(s) Paul I, Emili A
Citation(s) 36755019
Submission date Jan 19, 2022
Last update date Mar 02, 2023
Contact name Andrew Emili
Organization name Boston University
Department Biochemistry
Street address 72 East Concord St
City Boston
State/province MA
ZIP/Postal code 02118
Country USA
Platforms (1)
GPL19117 [miRNA-4] Affymetrix Multispecies miRNA-4 Array
Samples (10)
GSM5825508 Untreated_Control
GSM5825509 TGF_4_hours
GSM5825510 TGF_day_1
This SubSeries is part of SuperSeries:
GSE194019 Expression data from MCF10A cells treated with TGFβ for multiple time points
BioProject PRJNA798732

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

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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