Summary of study ST001638

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 IDST001638
Study TitleMetabolomics analysis of Vehicle (DMSO/PBS; (1:1) v/v) and DRB18 (10 mg/kg) treated A549 xenograft tumors
Study TypeAnticancer compound treatment experiment in vivo
Study SummaryA549 xenograft tumors were treated with (DMSO/PBS; (1:1) v/v) and DRB18 (10 mg/kg) for 5 weeks. The mice were then sacrificed and tumors were then excised. Tumors were then subjected to untargeted metabolomics analysis.
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
Phone7406033801
Submit Date2020-12-07
Num Groups2
Total Subjects20
Num Males20
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-04-01
Release Version1
Pratik Shriwas Pratik Shriwas
https://dx.doi.org/10.21228/M8X39Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


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:SU001715
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:4 weeks mice
Gender:Male
Animal Animal Supplier:Jackson Laboratory

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA150495Controlinvivo_10Control
SA150496Controlinvivo_11Control
SA150497Controlinvivo_1Control
SA150498Controlinvivo_8Control
SA150499Controlinvivo_12Control
SA150500Controlinvivo_9Control
SA150501Controlinvivo_7Control
SA150502Controlinvivo_2Control
SA150503Controlinvivo_4Control
SA150504Controlinvivo_3Control
SA150505Controlinvivo_5Control
SA150506Controlinvivo_6Control
SA150507DRB18invivo_10DRB18
SA150508DRB18invivo_9DRB18
SA150509DRB18invivo_12DRB18
SA150510DRB18invivo_8DRB18
SA150511DRB18invivo_11DRB18
SA150512DRB18invivo_1DRB18
SA150513DRB18invivo_3DRB18
SA150514DRB18invivo_2DRB18
SA150515DRB18invivo_4DRB18
SA150516DRB18invivo_5DRB18
SA150517DRB18invivo_6DRB18
SA150518DRB18invivo_7DRB18
Showing results 1 to 24 of 24

Collection:

Collection ID:CO001708
Collection Summary:A549 lung cancer xenograft tumors were obtained after sacrificing the mice. The tumors were then prepared according to the protocol described and metabolomics analysis was performed.
Sample Type:Tumor cells
Collection Method:Tumors were homogenized in a Beadbud homogenizer (Benchmark scientific) in a mixture of LC-MS grade ice-cold methanol and water (1:1; v/v). The supernatant was collected and sonicated in a water bath incubator for 15 minutes, followed by centrifugation at 13,000 rpm for 10 minutes and collection of the supernatant.
Collection Location:Homogenization vials
Collection Frequency:Once
Collection Duration:4-5 minutes
Volumeoramount Collected:1ml
Storage Conditions:-80℃
Collection Vials:Polypropylene 1.5 ml tubes
Storage Vials:Polypropylene 1.5 ml

Treatment:

Treatment ID:TR001728
Treatment Summary:Male NU/J nude mice of 3 to 4 weeks of age were purchased from The Jackson Laboratory and were fed with the Irradiated Teklad Global 19% protein rodent diet from Harlan Laboratories. The protocol for cell injection, treatment administration, weekly tumor measurement, animal euthanasia and final tumor measurements were performed as described previously (unless stated otherwise) (31). Tumor cell–injected mice were randomly divided into 2 groups: control group (n = 10) treated with PBS/DMSO (1:1, v/v) and 10 mg/kg (body weight) DRB18 treatment group (n = 10) dissolved in PBS/DMSO solution (1:1, v/v). Mice were given intraperitoneal injection with either PBS/DMSO vehicle or compound DRB18 (10 mg/kg) thrice a week for 5 weeks.
Treatment Protocol Filename:prats1988_20201207_Invivo_collection_and_preparation_method.docx
Treatment:Anticancer compound in xenograft tumors via i.p.
Treatment Compound:Control (DMSO/PBS; 1:1 v/v) and DRB18 (10mg/kg body weight dissolved in DMSO/PBS; 1:1 v/v)
Treatment Route:i.p.
Treatment Dose:10 mg/kg body weight
Treatment Dosevolume:100ul
Treatment Vehicle:DMSO/PBS (1:1; v/v)

Sample Preparation:

Sampleprep ID:SP001721
Sampleprep Summary:Tumors were homogenized in a Beadbud homogenizer (Benchmark scientific) in a mixture of LC-MS grade ice-cold methanol and water (1:1; v/v). The supernatant was collected and sonicated in a water bath incubator for 15 minutes, followed by centrifugation at 13,000 rpm for 10 minutes and collection of the supernatant. Supernatants collected from in vitro and in vivo extraction were then lyophilized using a speed vacuum evaporator. The samples were then dissolved into a mixture of LC-MS grade acetonitrile/water (1:1; v/v) for analysis.
Sampleprep Protocol Filename:prats1988_20201207_Invivo_collection_and_preparation_method.docx
Processing Method:Metabolite extraction; Quenching; speed vacuum evaporation
Processing Storage Conditions:-80℃
Extraction Method:Quenching with ice cold methanol
Extract Enrichment:Speed vaccum evaporator
Sample Resuspension:Acetonitrile/waster (1:1)

Combined analysis:

Analysis ID AN002680
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6545 QTOF
Ion Mode POSITIVE
Units Normalized abundances

Chromatography:

Chromatography ID:CH001974
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:none
Column Name:none
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
Solvent A:H2O with 0.1 % Formic acid
Solvent B:100 % acetonitrile
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002479
Analysis ID:AN002680
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Avin_C18_Pos.m methods was used. The data acquisition and processing was performed by masshunter software (Agilent Technologies).
Ion Mode:POSITIVE
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