Summary of Study ST001861

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001174. The data can be accessed directly via it's Project DOI: 10.21228/M8Z98Q This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001861
Study TitleParallelized multidimensional analytic framework, PAMAF, applied to mammalian cells uncovers novel regulatory principles in EMT
Study SummaryPainting a holistic picture of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. As opposed to ‘one omic at a time’, which provides an incomplete view on disease mechanisms, here we developed an experimental and analytics framework, PAMAF, to simultaneously acquire and analyze twelve omic modalities from the same set of samples, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; peptidome; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We applied PAMAF in a well-studied in vitro model of TGFβ-induced EMT to generate the EMT-ExMap dataset, cataloguing >61,000 expression profiles (>10,000 differential) over 12 days. PAMAF revealed that EMT is more complex than currently understood and identified numerous stage-specific mechanisms and vulnerabilities not captured in literature. Broad application of PAMAF will provide unprecedented insights into multifaceted biological processes relevant to human health and disease.
Boston University
Last NamePaul
First NameIndranil
Address71 East Concord St
Submit Date2021-06-22
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-11
Release Version1
Indranil Paul Indranil Paul application/zip

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Sample Preparation:

Sampleprep ID:SP001944
Sampleprep Summary:Each cell pellet was thawed on ice and resuspended in 500 μL ice-cold water by vortexing for 3 seconds and 500 μL of chilled (–80°C) 90% methanol + 10% chloroform solution was immediately added and vortexed for another 10 seconds and then kept on ice. Samples were incubated for 30 minutes at 4°C while rotating and then centrifuged at 800×g for 10 mins at 4°C. The supernatants were transferred to fresh tubes and centrifuged at 16000×g for 45 minutes at 4°C. The cleared supernatant containing metabolites were cleaned using a SPME (solid phase microextraction) protocol adopted from Mousavi et. al. (Mousavi et al., 2019), vacufuged to dryness and stored at –80°C. The cell pellets were used for protein extraction using GuHCl lysis method as described below.