Summary of Study ST002399
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 PR001533. The data can be accessed directly via it's Project DOI: 10.21228/M8J99C 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.
| Study ID | ST002399 |
| Study Title | Metabolomics of Adipocyte-Conditioned Media Compared to Stromal Cell- and Un-conditioned Media |
| Study Type | Untargeted MS |
| Study Summary | The metabolomics profiles of adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were analyzed by untargeted mass spectrometry. |
| Institute | Emory University |
| Department | Pediatrics |
| Laboratory | Joshua Chandler, PhD |
| Last Name | Chandler |
| First Name | Joshua |
| Address | 2015 Uppergate Drive NE, Atlanta, GA 30322 |
| joshua.chandler@emory.edu | |
| Phone | 404-727-3536 |
| Submit Date | 2022-10-21 |
| Num Groups | 3 (ACM vs SCM vs UCM) |
| Total Subjects | 5 replicates of each group (15 total) |
| Publications | submitted to JNCI |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001533 |
| Project DOI: | doi: 10.21228/M8J99C |
| Project Title: | The 'Omics of Obesity in B-cell Acute Lymphoblastic Leukemia |
| Project Summary: | The obesity pandemic currently affects over 70 million Americans and over 650 million individuals worldwide. In addition to increasing susceptibility to pathogenic infections (e.g., SARS-CoV-2 et al.), obesity promotes the development of many cancer subtypes and increases mortality rates in most cases. It has been demonstrated that, in the context of B-cell acute lymphoblastic leukemia (B-ALL), adipocytes promote multi-drug chemoresistance. Furthermore, it has been demonstrated that B-ALL cells exposed to the adipocyte secretome alter their metabolic states to circumvent chemotherapy-mediated cytotoxicity. To better understand how adipocytes impact the function of human B-ALL cells, we used an untargeted metabolomics mass spectroscopy approach to define adipocyte-induced changes in B-cells. These analyses revealed that the adipocyte secretome directly modulates programs in human B-ALL cells which are associated with metabolism. In all, our data increases our understanding of pathways which may promote chemoresistance in human B-ALL. |
| Institute: | Emory University |
| Department: | Pediatrics |
| Laboratory: | Joshua Chandler, PhD |
| Last Name: | Chandler |
| First Name: | Joshua |
| Address: | 2015 Uppergate Drive NE, Atlanta, GA 30322 |
| Email: | joshua.chandler@emory.edu |
| Phone: | 404-727-3536 |
| Funding Source: | This study was supported by funding for the CURE Childhood Cancer Foundation (Grant No. 001006916), Swim Across America (Grant No. 00103163), The Mark Foundation for Cancer Research (Grant No. 18-031-ASP), Emory University School of Medicine Bridge Funding (Grant No. 00098174), The American Cancer Society and Emory University Winship Cancer Institute Institutional Research Grant (Grant No. IRG-21-137-07-IRG) and the TREC Training Course (Grant No. R25CA203650) all awarded to Curtis J Henry. In additional, funding for Joshua Chandler included NIH R01 NR018666, R56 HL150658, and support from CF@LANTA, a component of Emory University and Children’s Healthcare of Atlanta. |
| Publications: | submitted to JNCI |
| Contributors: | Delaney K. Geitgey, Miyoung Lee, Kirsten A. Cottrill, Matthew B. Kilgore, Joshua D. Chandler, Curtis J. Henry |
Subject:
| Subject ID: | SU002488 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Subject Comments: | OP9 cells were left as stromal cells or were differentiated into adipocytes. These cells were allowed to condition media, with the media being the analyte in this study. |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Media |
|---|---|---|
| SA239050 | ACM3_Medium-1 | ACM |
| SA239051 | ACM4_Medium-1 | ACM |
| SA239052 | ACM5_Medium-1 | ACM |
| SA239053 | ACM1_Medium-1 | ACM |
| SA239054 | ACM2_Medium-1 | ACM |
| SA239055 | DMEM2_Medium-1 | DMEM |
| SA239056 | DMEM4_Medium-1 | DMEM |
| SA239057 | DMEM5_Medium-1 | DMEM |
| SA239058 | DMEM1_Medium-1 | DMEM |
| SA239059 | DMEM3_Medium-1 | DMEM |
| SA239065 | QC_Medium_full-MS-2-6 | n/a |
| SA239066 | QC_Medium_full-MS-3-1 | n/a |
| SA239067 | Blank2-2 | n/a |
| SA239068 | NIST-2 | n/a |
| SA239069 | Blank1-2 | n/a |
| SA239070 | AA-H_1-1000 | n/a |
| SA239071 | AA-H_1-1000-2 | n/a |
| SA239072 | Blank4-2 | n/a |
| SA239073 | Blank3-3 | n/a |
| SA239074 | Blank3-4 | n/a |
| SA239075 | QC_Medium_full-MS-3-3 | n/a |
| SA239076 | Blank2-3 | n/a |
| SA239077 | Blank1-3 | n/a |
| SA239078 | QC_Medium_full-MS-3-2 | n/a |
| SA239079 | Blank4-1 | n/a |
| SA239080 | NIST | n/a |
| SA239081 | QC_Medium_ddMS2-1-5 | n/a |
| SA239082 | QC_Medium_full-MS-1-6 | n/a |
| SA239083 | QC_Medium_full-MS-2-1 | n/a |
| SA239084 | QC_Medium_ddMS2-1-4 | n/a |
| SA239085 | QC_Medium-1-3 | n/a |
| SA239086 | QC_Medium-1-1 | n/a |
| SA239087 | QC_Medium-1-2 | n/a |
| SA239088 | Blank3-1 | n/a |
| SA239089 | Blank1-4 | n/a |
| SA239090 | Blank2-1 | n/a |
| SA239091 | Blank3-2 | n/a |
| SA239092 | QC_Medium_full-MS-2-4 | n/a |
| SA239093 | QC_Medium_full-MS-2-3 | n/a |
| SA239094 | QC_Medium_full-MS-2-2 | n/a |
| SA239095 | Blank2-4 | n/a |
| SA239096 | Blank1-1 | n/a |
| SA239097 | QC_Medium_full-MS-2-5 | n/a |
| SA239060 | SCM5_Medium-1 | SCM |
| SA239061 | SCM3_Medium-1 | SCM |
| SA239062 | SCM4_Medium-1 | SCM |
| SA239063 | SCM2_Medium-1 | SCM |
| SA239064 | SCM1_Medium-1 | SCM |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO002481 |
| Collection Summary: | OP-9 bone marrow stromal cells were maintained in α-MEM (cat#15-012-CV, Corning, Glendale, AZ) supplemented with 20% FBS. For adipocyte differentiation, 105 OP-9 cells were plated in 6-well plates in DMEM (cat#10-017-CV, Corning, Glendale, AZ) supplemented with 10% FBS as previously described [18, 26]. After 24 hours of culture, the media was removed and switched to differentiation media which is composed of α-MEM supplemented with 1.8mM oleate (cat#O7501, Sigma, St. Louis, MO) bound to BSA (cat#A6003, Sigma, St. Louis, MO) with molar ratio 5.5:1 along with 175nM insulin (cat#I6634, Sigma, St. Louis, MO) and 0.2% FBS. ACM was collected after 3 days of differentiation and used in the experiments describe in this study. For SCM, OP-9 cells were plated in DMEM supplemented with 10% FBS and conditioned media were collected on day 3 of culture. |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002500 |
| Treatment Summary: | Cells and media were not treated with anything |
Sample Preparation:
| Sampleprep ID: | SP002494 |
| Sampleprep Summary: | Media samples (50 µL) were mixed with acetonitrile (Sigma) (100 µL) and vortexed. All samples were incubated 30 min on ice and centrifuged at 20,627 g for 10 min at 4 ˚C. The supernatant was transferred to autosampler vials (ThermoFisher) held at 4 ˚C for LC-MS acquisition. |
| Processing Storage Conditions: | On ice |
Chromatography:
| Chromatography ID: | CH002892 |
| Chromatography Summary: | A VanquishTM Horizon Binary ultrahigh performance liquid chromatography system coupled to a Q Exactive High Field Hybrid Orbitrap mass spectrometer (ThermoFisher) was used for data collection. A SeQuant® ZIC-HILIC column (Millipore Sigma, 3.5 µm, 100 Å, 150 x 2.1 mm, PEEK) was pumped with a mixture of mobile phases of 0.1% formic acid in water (mobile phase A) or 0.1% formic acid in acetonitrile (mobile phase B) (all reagents from Millipore Sigma). The column was equilibrated with 90% B for 8.3 min at 0.25 mL/min, after which 2.5 mL of extracted sample was injected. After this, a gradient ran from 90% to 20% B over 17.5, then was held at 20% B at 0.35 mL/min for 7.5 min. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1mm,3.5um) |
| Flow Gradient: | The column was equilibrated with 90% B for 8.3 min at 0.25 mL/min, after which 2.5 mL of extracted sample was injected. After this, a gradient ran from 90% to 20% B over 17.5 min, then was held at 20% B at 0.35 mL/min for 7.5 min |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN003906 |
| Laboratory Name: | Joshua Chandler, PhD |
| Analysis Type: | MS |
| Acquisition Date: | 2018-2019 |
| Software Version: | Compound Discoverer 3.3 |
| Operator Name: | Matthew Kilgore, PhD |
| Detector Type: | Orbitrap |
| Chromatography ID: | CH002892 |
| Num Factors: | 4 |
| Num Metabolites: | 167 |
| Units: | Peak area |
