PXD031071

PXD031071 is an original dataset announced via ProteomeXchange.

Title	Parallelized multidimensional analytic framework applied to mammalian cells uncovers novel regulatory principles in EMT
Description	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.
HostingRepository	PRIDE
AnnounceDate	2022-11-14
AnnouncementXML	Submission_2022-11-14_05:27:32.408.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	IndranilPaul
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-19 02:49:05	ID requested
⏵ 1	2022-11-14 05:27:32	announced

Dataset with its publication pending

submitter keyword: Multiomics, TGFbeta, EMT,MCF10A, Mass spectrometry, Proteomics

AndrewEmili
contact affiliation	Director, Center for Network Systems Biology Departments of Biochemistry & Biology Boston University, Boston, MA, USA
contact email	aemili@bu.edu
lab head
IndranilPaul
contact affiliation	Boston University
contact email	indranil@bu.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/11/PXD031071

PRIDE project URI

• PRIDE
  1. PXD031071
     1. Label: PRIDE project
     2. Name: Parallelized multidimensional analytic framework applied to mammalian cells uncovers novel regulatory principles in EMT