Summary of Study ST001779
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 PR001132. The data can be accessed directly via it's Project DOI: 10.21228/M8CQ5F 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 | ST001779 |
| Study Title | Untargeted Metabolomics analysis of A549 treated with 0.5 mM extracellular ATP and 10 ng/ml TGF-beta |
| Study Type | Untargeted metabolomics analysis in lung cancer cells |
| Study Summary | Control, 0.5 mM extracellular ATP and 10 ng/ml TGF-beta were used to treated 5 million A549 lung cancer cells in vitro for 2, 6 and 12 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 extracellular ATP and TGF-beta (a known EMT inducer). |
| Institute | Ohio University |
| Department | Biological Sciences |
| Laboratory | Dr. Xiaozhuo Chen, Edison biotechnology Institute |
| Last Name | Shriwas |
| First Name | Pratik |
| Address | Room 425, Parks Hall, College of Pharmacy, Ohio State University, Columbus Ohio. 43210 |
| ps774614@ohio.edu | |
| Phone | 7406033801 |
| Submit Date | 2021-04-04 |
| Num Groups | 7 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-05-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001132 |
| Project DOI: | doi: 10.21228/M8CQ5F |
| Project Title: | Untargeted metabolomics analysis of A549 cancer cells treated in control, 0.5 mM ATP and 10 ng/ml TGF-beta for 2, 6 and 12 hours |
| Project Type: | Untargeted quantitative metabolomics analysis |
| Project Summary: | A549 lung cancer cells were treated in vitro with control, 0.5 mM ATP and 10 ng/ml TGF-beta for 2, 6 and 12 hours 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: | Room 425, Parks Hall, College of Pharmacy, Ohio State University, Columbus Ohio. 43210 |
| Email: | ps774614@ohio.edu |
| Phone: | 7406033801 |
| Funding Source: | This study was funded by NIH R15 grant CA242177-01 to Dr. Xiaozhuo Chen. |
Subject:
| Subject ID: | SU001856 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Biosource Or Supplier: | ATCC |
| Cell Strain Details: | Human Lung epithelial A549 cancer cells |
| Cell Passage Number: | 10 |
| Cell Counts: | 5 million cells |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA165025 | 12h ATP_2 | 12h ATP |
| SA165026 | 12h ATP_3 | 12h ATP |
| SA165027 | 12h ATP_6 | 12h ATP |
| SA165028 | 12h ATP_1 | 12h ATP |
| SA165029 | 12h ATP_4 | 12h ATP |
| SA165030 | 12h ATP_5 | 12h ATP |
| SA165031 | 12h TGF-β_4 | 12h TGF-β |
| SA165032 | 12h TGF-β_3 | 12h TGF-β |
| SA165033 | 12h TGF-β_2 | 12h TGF-β |
| SA165034 | 12h TGF-β_5 | 12h TGF-β |
| SA165035 | 12h TGF-β_6 | 12h TGF-β |
| SA165036 | 12h TGF-β_1 | 12h TGF-β |
| SA165037 | 2h ATP_4 | 2h ATP |
| SA165038 | 2h ATP_1 | 2h ATP |
| SA165039 | 2h ATP_3 | 2h ATP |
| SA165040 | 2h ATP_5 | 2h ATP |
| SA165041 | 2h ATP_2 | 2h ATP |
| SA165042 | 2h ATP_6 | 2h ATP |
| SA165043 | 2h TGF-β_4 | 2h TGF-β |
| SA165044 | 2h TGF-β_5 | 2h TGF-β |
| SA165045 | 2h TGF-β_6 | 2h TGF-β |
| SA165046 | 2h TGF-β_2 | 2h TGF-β |
| SA165047 | 2h TGF-β_3 | 2h TGF-β |
| SA165048 | 2h TGF-β_1 | 2h TGF-β |
| SA165049 | 6h ATP_4 | 6h ATP |
| SA165050 | 6h ATP_3 | 6h ATP |
| SA165051 | 6h ATP_1 | 6h ATP |
| SA165052 | 6h ATP_2 | 6h ATP |
| SA165053 | 6h TGF-β_4 | 6h TGF-β |
| SA165054 | 6h TGF-β_1 | 6h TGF-β |
| SA165055 | 6h TGF-β_3 | 6h TGF-β |
| SA165056 | 6h TGF-β_2 | 6h TGF-β |
| SA165057 | Control_2 | Control |
| SA165058 | Control_3 | Control |
| SA165059 | Control_4 | Control |
| SA165060 | Control_1 | Control |
| Showing results 1 to 36 of 36 |
Collection:
| Collection ID: | CO001849 |
| Collection Summary: | A549 lung cancer cells were treated with control, ATP, TGF-beta and then collected according to sample preparation protocol. |
| Collection Protocol Filename: | Collection 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 |
| Collection Tube Temp: | 4C |
| Tissue Cell Quantity Taken: | 5 million |
Treatment:
| Treatment ID: | TR001869 |
| Treatment Summary: | 5 million A549 cells were treated with control (no treatment), 0.5 mM ATP or 10 ng/ml TGF-beta for 2, 6 and 12 hours. |
| Treatment: | In vitro treatment with small molecules |
| Treatment Compound: | 0.5 mM ATP and 10 ng/ml TGF-beta |
| Treatment Dosevolume: | 10 ml DMEM media containing appropriate compounds |
| 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 2, 6 and 12 hours |
| Cell Pct Confluence: | 80% |
| Cell Media Lastchanged: | NA |
Sample Preparation:
| Sampleprep ID: | SP001862 |
| Sampleprep Summary: | 5 × 106 A549 cells were treated with control (no treatment), 0.5 mM ATP or 10 ng/ml TGF-beta for 2, 6 and 12 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 vacuum evaporator. The samples were then dissolved into a mixture of acetonitrile/water (1:1; v/v). |
| Sampleprep Protocol Filename: | Sample preparation protocol |
| Processing Method: | CEll scrapping Quenching |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Quenching with Ice cold methanol |
| Extract Enrichment: | Speed vaccum evaporator |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Acetonitrile/water (1:1) |
Combined analysis:
| Analysis ID | AN002888 | AN002889 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 | Agilent 1290 |
| Column | Poroshell 120 SB-C18 (100 x 2.1mm,2.7um) | Poroshell 120 SB-C18 (100 x 2.1mm,2.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6545 QTOF | Agilent 6545 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | normalized | normalized |
Chromatography:
| Chromatography ID: | CH002141 |
| 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 (100 x 2.1mm,2.7um) |
| 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: | Reversed phase |
MS:
| MS ID: | MS002681 |
| Analysis ID: | AN002888 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Masshunter software was used to collect the raw data. Progenesis was used for peak intergration. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002682 |
| Analysis ID: | AN002889 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Masshunter software was used to collect the raw data. Progenesis was used for peak intergration. |
| Ion Mode: | NEGATIVE |
