Summary of study ST001610

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 PR001035. The data can be accessed directly via it's Project DOI: 10.21228/M8X39Q This work is supported by NIH grant, U2C- DK119886.

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Study IDST001610
Study TitleControl (DMSO 0.1%; v/v) and 10 µM DRB18 treated A549 lung cancer cells in vitro for 48 hours
Study TypeAnticancer compound treatment experiment
Study SummaryControl (DMSO 0.1%; v/v) and 10 µM DRB18 were used to treated 5 million A549 lung cancer cells in vitro for 48 hours. The untargeted metabolomics analysis was performed on the cell lysates. The main objective of the study was to determine changes in metabolite abundances in lung cancer after treatment with DRB18, an inhibitor of glucose transporter proteins.
Institute
Ohio University
DepartmentBiological Sciences
LaboratoryDr. Xiaozhuo Chen, Edison biotechnology Institute
Last NameShriwas
First NamePratik
Address172 Water Tower, Building 25, The Ridges, Konnekar Research Centerm Athens Ohio - 45701, USA
Emailps774614@ohio.edu
Phone740-603-3801
Submit Date2020-11-08
Num Groups2
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2020-12-09
Release Version1
Pratik Shriwas Pratik Shriwas
https://dx.doi.org/10.21228/M8X39Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001035
Project DOI:doi: 10.21228/M8X39Q
Project Title:Untargeted metabolomics analysis of A549 cancer cells treated in vitro and in vivo by control (DMSO) or DRB18
Project Type:Untargeted quantitative metabolomics analysis
Project Summary:DR18, a novel anticancer compound was used to A549 lung cancer cells in vitro and A549 cell line derived xenograft tumors in vivo in nude mice. The untargeted metabolomics data was generated from these studies.
Institute:Ohio University
Department:Biological Sciences
Laboratory:Dr. Xiaozhuo Chen, Edison biotechnology Institute
Last Name:Shriwas
First Name:Pratik
Address:172 Water Tower, Building 25, The Ridges, Konnekar Research Centerm Athens Ohio - 45701, USA
Email:ps774614@ohio.edu
Phone:740-603-3801
Contributors:Campus Chemical Instrument Center, Ohio State University

Subject:

Subject ID:SU001687
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Strain Details:Human Lung epithelial A549 cancer cells

Factors:

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

mb_sample_id local_sample_id Treatment
SA136748Controlinvitro_8Control
SA136749Controlinvitro_9Control
SA136750Controlinvitro_1Control
SA136751Controlinvitro_6Control
SA136752Controlinvitro_7Control
SA136753Controlinvitro_2Control
SA136754Controlinvitro_4Control
SA136755Controlinvitro_3Control
SA136756Controlinvitro_5Control
SA136757DRB18invitro_7DRB18
SA136758DRB18invitro_8DRB18
SA136759DRB18invitro_9DRB18
SA136760DRB18invitro_6DRB18
SA136761DRB18invitro_1DRB18
SA136762DRB18invitro_2DRB18
SA136763DRB18invitro_3DRB18
SA136764DRB18invitro_4DRB18
SA136765DRB18invitro_5DRB18
Showing results 1 to 18 of 18

Collection:

Collection ID:CO001680
Collection Summary:A549 lung cancer cells were treated with control or DRB18 and then collected according to sample preparation protocol.
Sample Type:Lung
Collection Method:Ice cold methanol (80%) using cell scrappers
Collection Location:150mm dish
Collection Frequency:Once
Collection Duration:1-2 sec
Volumeoramount Collected:1 ml
Storage Conditions:-80℃
Collection Vials:Polypropylene 1.5 ml tubes
Storage Vials:Polypropylene 1.5 ml
Tissue Cell Quantity Taken:5 million

Treatment:

Treatment ID:TR001700
Treatment Summary:5 million A549 cells were treated with or without DRB18 (n=3) for 48 hours.
Treatment:Anticancer compound in vitro
Treatment Compound:Control (DMSO; 0.1% v/v) and DRB18
Treatment Dosevolume:10 ml DMEM media containing appropriate compounds
Treatment Vehicle:DMSO
Cell Storage:37C; 5% CO2 incubator
Cell Growth Container:150 mm Dish tissue culture treated
Cell Media:DMEM (10% FBS; 1% Pen/Strep)
Cell Harvesting:after 48 hours
Cell Pct Confluence:80%
Cell Media Lastchanged:NA

Sample Preparation:

Sampleprep ID:SP001693
Sampleprep Summary:5 × 106 A549 cells were treated with or without DRB18 for 48 hours. After treatment, cells were washed twice with deionized water and polar metabolites were then extracted with cryogenically cold 80% methanol/water mixture. LC-MS grade water, methanol, and acetonitrile (Fischer Scientific, PA, USA) were used. Methanol-extracted samples were then sonicated in cycles of sonication phase and rest phase for 10 minutes (5 second sonication phase and 10 seconds halt). The samples were then centrifuged at 13,000 rpm for 10 minutes and supernatant was then collected. Supernatants collected from in vitro and in vivo extraction were then lyophilized. Briefly, the supernatant was then lyophilized by using a speed vaccum evaporator. The samples were then dissolved into a mixture of acetonitrile/water (1:1; v/v).
Processing Method:Quenching
Processing Storage Conditions:-80℃
Extraction Method:Quenching with Ice cold methanol
Extract Enrichment:Speed vaccum evaporator
Extract Storage:-80℃
Sample Resuspension:Acetonitrile/waster (1:1)

Combined analysis:

Analysis ID AN002644
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290
Column Poroshell 120 SB-C18 (2.1 x 100 mm x 2.7 µm)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6545 QTOF
Ion Mode POSITIVE
Units Normalized abundances

Chromatography:

Chromatography ID:CH001953
Chromatography Summary:The entire LC/MS-MS experiment was performed in the Campus Chemical Instrumentation Center’s Mass Spectrometry and Proteomics facility at The Ohio State University. Lyophilized samples were dissolved in equal amounts of LC-MS grade water and acetonitrile and run with LC/MS-MS analysis, using an untargeted metabolomics approach by utilizing Agilent Q-TOF 6545 mass spectrometer connected to an Agilent 1290 UHPLC system with a Poroshell 120 SB-C18 (2 x 100 mm, 2.7 µm particle size) column. The LC gradient consisted of solvent A, H2O with 0.1 % Formic acid, and solvent B, 100 % acetonitrile at a 200 µL/min flow rate with an initial 2 % solvent B with a linear ramp to 95 % B at 15 min, holding at 95% B for 1 minutes, and back to 2 % B from 16 min and equilibration of 2 % B until min 32. A 5 µL volume sample was injected for each run and the top 5 ions were selected for data-dependent analysis with a 15 second exclusion window.
Instrument Name:Agilent 1290
Column Name:Poroshell 120 SB-C18 (2.1 x 100 mm x 2.7 µm)
Column Pressure:800 bar
Column Temperature:40
Flow Gradient:an initial 2 % solvent B with a linear ramp to 95 % B at 15 min, holding at 95% B for 1 minutes, and back to 2 % B from 16 min and equilibration of 2 % B until min 32.
Flow Rate:200 µL/min
Sample Injection:5 µL
Solvent A:H2O with 0.1 % Formic acid
Solvent B:100 % acetonitrile
Capillary Voltage:500 V
Chromatography Type:Reversed phase

MS:

MS ID:MS002456
Analysis ID:AN002644
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Masshunter software was used to collect the raw data
Ion Mode:POSITIVE
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