Summary of Study ST002052

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 PR001298. The data can be accessed directly via it's Project DOI: 10.21228/M8XQ3N 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 IDST002052
Study TitleMulti-omic Attributes and Unbiased Computational Modeling for the Prediction of Immunomodulatory Potency of Mesenchymal Stromal Cells
Study SummaryMesenchymal stromal cells (MSCs) are “living medicines” that continue to be evaluated in clinical trials to treat various clinical indications, yet remain unapproved. Because these cell therapies can be harvested from different tissue sources, are manufactured ex vivo, and are composed of highly responsive cells from donors of varying demographics, significant complexities limit the current understanding and advancements to clinical practice. However, we propose a model workflow used to overcome challenges by identifying multi-omic features that can serve as predictive therapeutic outcomes of MSCs. Here, features were identified using unbiased symbolic regression and machine learning models that correlated multi-omic datasets to results from in vitro functional assays based on putative mechanisms of action of MSCs. Together, this study provides a compelling framework for achieving the identification of candidate CQAs specific to MSCs that may help overcome current challenges, advancing MSCs to broad clinical use. This upload contain the metabolomic datasets, which were correlated with quality metrics, such as potency.
Institute
Georgia Institute of Technology
LaboratorySystem Mass Spectrometry Core
Last NameGaul
First NameDavid
Address311 Ferst Drive Atlanta, GA 30332
Emaildavid.gaul@chemistry.gatech.edu
Phone4048943870
Submit Date2022-01-06
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-01-06
Release Version1
David Gaul David Gaul
https://dx.doi.org/10.21228/M8XQ3N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001298
Project DOI:doi: 10.21228/M8XQ3N
Project Title:Multi-omic attributes and unbiased computational modeling for the prediction of immunomodulatory potency of mesenchymal stromal cells
Project Summary:Mesenchymal stromal cells (MSCs) are “living medicines” that continue to be evaluated in clinical trials to treat various clinical indications, yet remain unapproved. Because these cell therapies can be harvested from different tissue sources, are manufactured ex vivo, and are composed of highly responsive cells from donors of varying demographics, significant complexities limit the current understanding and advancements to clinical practice. However, we propose a model workflow used to overcome challenges by identifying multi-omic features that can serve as predictive therapeutic outcomes of MSCs. Here, features were identified using unbiased symbolic regression and machine learning models that correlated multi-omic datasets to results from in vitro functional assays based on putative mechanisms of action of MSCs. Together, this study provides a compelling framework for achieving the identification of candidate CQAs specific to MSCs that may help overcome current challenges, advancing MSCs to broad clinical use. This upload contains the metabolomic dataset which were correlated with quality metrics, such as potency.
Institute:Georgia Institute of Technology
Last Name:Gaul
First Name:David
Address:311 Ferst Drive Atlanta, GA 30332
Email:david.gaul@chemistry.gatech.edu
Phone:4048943870

Subject:

Subject ID:SU002134
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Factor
SA193618BM5_1MSC_BoneMarrow
SA193619BM5_2MSC_BoneMarrow
SA193620BM4_3MSC_BoneMarrow
SA193621BM4_1MSC_BoneMarrow
SA193622BM3_3MSC_BoneMarrow
SA193623BM5_3MSC_BoneMarrow
SA193624BM4_2MSC_BoneMarrow
SA193625BM6_1MSC_BoneMarrow
SA193626BM7_2MSC_BoneMarrow
SA193627BM7_3MSC_BoneMarrow
SA193628BM7_1MSC_BoneMarrow
SA193629BM6_3MSC_BoneMarrow
SA193630BM6_2MSC_BoneMarrow
SA193631BM3_1MSC_BoneMarrow
SA193632BM3_2MSC_BoneMarrow
SA193633BM1_2MSC_BoneMarrow
SA193634BM2_3MSC_BoneMarrow
SA193635BM2_1MSC_BoneMarrow
SA193636BM1_1MSC_BoneMarrow
SA193637BM2_2MSC_BoneMarrow
SA193638CT1MSC_CordTissue
SA193639CT2MSC_CordTissue
SA193640CT3MSC_CordTissue
SA193641Blank05NA
SA193642Blank04NA
SA193643Blank02NA
SA193644QC01NA
SA193645QC04NA
SA193646QC07NA
SA193647Blank01NA
SA193648QC06NA
SA193649QC05NA
SA193650QC03NA
SA193651QC02NA
Showing results 1 to 34 of 34

Collection:

Collection ID:CO002127
Collection Summary:Bone Marrow derived Mesenchymal Stromal Cells were purchased from RoosterBio, and the cord tissue derived Mesenchymal Stromal Cells were from Duke University School of Medicine.
Sample Type:Stem cells

Treatment:

Treatment ID:TR002146
Treatment Summary:BM-MSCs were expanded in either regular media or xeno-free media, while the CT-MSCs were expanded in xeno-free media. Harvested cells were resuspended in CryoStor CS5.

Sample Preparation:

Sampleprep ID:SP002140
Sampleprep Summary:Metabolites were extracted using a modified bligh-Dyer on 1 million MSC pellet with bead homogenization.The Aqueous layer was dried, reconstituted with 80% MeOH with internal standards prior to analysis. the organic layer was also dried, reconstituted with IPA with internal standards prior to analysis

Combined analysis:

Analysis ID AN003339 AN003340 AN003341 AN003342
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Thermo Accucore C30 (150 x 2.1mm,2.6um) Thermo Accucore C30 (150 x 2.1mm,2.6um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap orbitrap and ion trap orbitrap and ion trap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH002473
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C30 (150 x 2.1mm,2.6um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002474
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS003108
Analysis ID:AN003339
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Compound Discoverer used to process
Ion Mode:POSITIVE
  
MS ID:MS003109
Analysis ID:AN003340
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Compound Discoverer used to process
Ion Mode:NEGATIVE
  
MS ID:MS003110
Analysis ID:AN003341
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:orbitrap and ion trap
MS Type:ESI
MS Comments:Compound Discoverer used to process
Ion Mode:POSITIVE
  
MS ID:MS003111
Analysis ID:AN003342
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:orbitrap and ion trap
MS Type:ESI
MS Comments:Compound Discoverer used to process
Ion Mode:NEGATIVE
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