Summary of Study ST001861

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, 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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 ID	ST001861
Study Title	Parallelized multidimensional analytic framework, PAMAF, applied to mammalian cells uncovers novel regulatory principles in EMT
Study Summary	Painting 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.
Institute	Boston University
Last Name	Paul
First Name	Indranil
Address	71 East Concord St
Email	indranil@bu.edu
Phone	6177929632
Submit Date	2021-06-22
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2022-11-11
Release Version	1

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Treatment:

Treatment ID:	TR001950
Treatment Summary:	Human breast epithelial MCF10A cells were kindly provided by Prof. Senthil Muthuswamy (Beth Israel Deaconess Medical Center, Harvard Medical School). Cells were cultured in DMEM/F-12 supplemented with 5% Horse serum, EGF 20 ng/mL (Sigma), Insulin 10 μg/mL (Sigma), Hydrocortisone 0.5 mg/mL (Sigma), Cholera toxin 100 ng/mL (Sigma), 100 units/mL Penicillin and 100 μg/mL Streptomycin (HyClone) and grown at 37°C in a humidified incubator with 5% CO2. To induce EMT, cells were stimulated with 10 ng/mL TGF-β1 (Invivogen) and treatments were staggered such that all cells (plates) were harvested at the same time. To minimize cross-contamination (EV & Sec) and promiscuous background signaling (particularly for Phos), cells were cultured in serum-free conditions for 16 hours prior to harvesting. At the time of harvest, conditioned media were first transferred to fresh 50 mL tubes and kept on ice. Cells were washed once with ice-cold PBS and scraped off the plates in ice-cold PBS. Each sample was then distributed into multiple aliquots for multi-omics extractions, centrifuged at 800×g for 5 minutes at 4°C and stored as dry pellets at –80°C. Live cells were imaged in their culture vessels before harvesting using ZOE fluorescent cell imager (Bio-Rad).

Treatment ID:

TR001950

Treatment Summary:

Human breast epithelial MCF10A cells were kindly provided by Prof. Senthil Muthuswamy (Beth Israel Deaconess Medical Center, Harvard Medical School). Cells were cultured in DMEM/F-12 supplemented with 5% Horse serum, EGF 20 ng/mL (Sigma), Insulin 10 μg/mL (Sigma), Hydrocortisone 0.5 mg/mL (Sigma), Cholera toxin 100 ng/mL (Sigma), 100 units/mL Penicillin and 100 μg/mL Streptomycin (HyClone) and grown at 37°C in a humidified incubator with 5% CO2. To induce EMT, cells were stimulated with 10 ng/mL TGF-β1 (Invivogen) and treatments were staggered such that all cells (plates) were harvested at the same time. To minimize cross-contamination (EV & Sec) and promiscuous background signaling (particularly for Phos), cells were cultured in serum-free conditions for 16 hours prior to harvesting. At the time of harvest, conditioned media were first transferred to fresh 50 mL tubes and kept on ice. Cells were washed once with ice-cold PBS and scraped off the plates in ice-cold PBS. Each sample was then distributed into multiple aliquots for multi-omics extractions, centrifuged at 800×g for 5 minutes at 4°C and stored as dry pellets at –80°C. Live cells were imaged in their culture vessels before harvesting using ZOE fluorescent cell imager (Bio-Rad).