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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001638 |
| Study Title | Metabolomics analysis of Vehicle (DMSO/PBS; (1:1) v/v) and DRB18 (10 mg/kg) treated A549 xenograft tumors |
| Study Type | Anticancer compound treatment experiment in vivo |
| Study Summary | A549 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 |
| 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 |
| ps774614@ohio.edu | |
| Phone | 7406033801 |
| Submit Date | 2020-12-07 |
| Num Groups | 2 |
| Total Subjects | 20 |
| Num Males | 20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-04-01 |
| Release Version | 1 |
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 |
|---|---|---|
| SA150495 | Controlinvivo_10 | Control |
| SA150496 | Controlinvivo_11 | Control |
| SA150497 | Controlinvivo_1 | Control |
| SA150498 | Controlinvivo_8 | Control |
| SA150499 | Controlinvivo_12 | Control |
| SA150500 | Controlinvivo_9 | Control |
| SA150501 | Controlinvivo_7 | Control |
| SA150502 | Controlinvivo_2 | Control |
| SA150503 | Controlinvivo_4 | Control |
| SA150504 | Controlinvivo_3 | Control |
| SA150505 | Controlinvivo_5 | Control |
| SA150506 | Controlinvivo_6 | Control |
| SA150507 | DRB18invivo_10 | DRB18 |
| SA150508 | DRB18invivo_9 | DRB18 |
| SA150509 | DRB18invivo_12 | DRB18 |
| SA150510 | DRB18invivo_8 | DRB18 |
| SA150511 | DRB18invivo_11 | DRB18 |
| SA150512 | DRB18invivo_1 | DRB18 |
| SA150513 | DRB18invivo_3 | DRB18 |
| SA150514 | DRB18invivo_2 | DRB18 |
| SA150515 | DRB18invivo_4 | DRB18 |
| SA150516 | DRB18invivo_5 | DRB18 |
| SA150517 | DRB18invivo_6 | DRB18 |
| SA150518 | DRB18invivo_7 | DRB18 |
| 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 | Unspecified |
| 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: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Unspecified |
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 |
