Summary of Study ST000134
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 PR000119. The data can be accessed directly via it's Project DOI: 10.21228/M86C76 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000134 |
| Study Title | Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy |
| Study Type | Metabolite level response after treatment with organoselenium |
| Study Summary | Metabolomics analysis was performed on DU145 prostate cancer cells and PNT1A non-tumorigenic prostate cells after treatment with selenomethionine and Se-methylselenocysteine using 800 MHz Bruker NMR spectrometer on 18 cell samples. |
| Institute | Purdue University |
| Department | Biology/Chemistry |
| Laboratory | Biology/Chemistry |
| Last Name | Isaac-Lam |
| First Name | Meden |
| Address | 1401 S US Hwy 421, Westville, IN 46391 |
| isaaclam@pnc.edu | |
| Phone | 219-785-5776 |
| Submit Date | 2015-01-13 |
| Num Groups | 6 |
| Total Subjects | 18 |
| Raw Data Available | No |
| Analysis Type Detail | NMR |
| Release Date | 2015-01-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000119 |
| Project DOI: | doi: 10.21228/M86C76 |
| Project Title: | Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy |
| Project Type: | Metabolomics by 1H NMR |
| Project Summary: | 1H NMR data of prostate cells treated with selenium showed a decreasing trend in metabolite levels with the largest change exhibited by creatine mainly due to disrupted energy metabolism, and probably due to loss of structural integrity combined with external dissipation of metabolites. Lactate, choline-containing compounds, and glycine levels increased depending on the type of selenium used and the cell type. Principal component analysis (PCA) showed that SeM-treated cells can be distinguished from SeMSC-treated cells, and DU145 PCa from PNT1A normal cells. |
| Institute: | Purdue University |
| Department: | Biology/Chemistry |
| Laboratory: | Biology/Chemistry Dept |
| Last Name: | Isaac-Lam |
| First Name: | Meden |
| Address: | 1401 S US Hwy 421 Westville, Indiana USA |
| Email: | isaaclam@pnc.edu |
| Phone: | 1-219-785-5776 |
| Funding Source: | Indiana Academy of Science |
Subject:
| Subject ID: | SU000153 |
| Subject Type: | Human cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Biosource Or Supplier: | ATCC, Sigma |
| Cell Strain Details: | DU145 prostate cancer, PNT1A prostate nontumor |
| Subject Comments: | 10 |
| Cell Primary Immortalized: | Immortalized |
| Cell Passage Number: | 10 |
| Cell Counts: | 10 |
| Species Group: | Human |
Factors:
Subject type: Human cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Prostate Cell Line |
|---|---|---|---|
| SA007395 | SeM (DU145) | SeM | DU145 |
| SA007396 | SeM (PNT1A) | SeM | PNT1A |
| SA007397 | SeMSC (DU145) | SeMSC | DU145 |
| SA007398 | SeMSC (PNT1A) | SeMSC | PNT1A |
| Showing results 1 to 4 of 4 |
Collection:
| Collection ID: | CO000137 |
| Collection Summary: | After incubation for 24 hrs, cells were washed twice with 0.5 mL PBS in D2O (Cambridge Isotope Laboratories). D2O (0.7 mL) was again added to each petri dish and cells were gently scraped from the surface with a sterile cell scraper. A volume of 0.7 mL of the harvested cell suspension was transferred into a 5 mm NMR tube and 10 mL of 100 mM TMSP in D2O was added to each tube. |
| Sample Type: | cell line |
| Collection Method: | scraping cells from flask |
| Collection Location: | lab |
| Collection Frequency: | once a week |
| Volumeoramount Collected: | 0.7 mL per dish |
| Storage Conditions: | in ice |
| Collection Tube Temp: | in ice |
Treatment:
| Treatment ID: | TR000155 |
| Treatment Summary: | Cells were grown to 80% confluence in Petri dishes (50 mm in diameter) in 4.5% CO2 at 37 OC for 5-6 days for full attachment to the substratum. After aspirating the old growth medium, 3 mL of SeM or SeMSC (300 mM) in fresh pre-warmed medium at 37 ºC was added to each dish. |
| Treatment Compound: | Selenomethionine / Se-methylselenocysteine |
| Treatment Dose: | 300 mM |
| Treatment Dosevolume: | 3 mL |
| Treatment Doseduration: | 24 hrs |
| Treatment Vehicle: | dissolved in culture media |
| Cell Storage: | incubator |
| Cell Growth Container: | petri dish (Corning) |
| Cell Growth Config: | monolayer, adherent |
| Cell Growth Rate: | 5-6 days |
| Cell Inoc Proc: | trypsinized, then subculture |
| Cell Media: | RPMI, EMEM |
| Cell Envir Cond: | 37 C, 4.5% CO2 incubator |
| Cell Harvesting: | after trypsinization |
| Cell Pct Confluence: | 80% |
| Cell Media Lastchanged: | 2-3 days |
Sample Preparation:
| Sampleprep ID: | SP000150 |
| Sampleprep Summary: | Cells were grown to 80% confluence in Petri dishes (50 mm in diameter) in 4.5% CO2 at 37 OC for 5-6 days for full attachment to the substratum. After aspirating the old growth medium, 3 mL of SeM or SeMSC (300 mM) in fresh pre-warmed medium at 37 ºC was added to each dish. After incubation for 24 hrs, cells were washed twice with 0.5 mL PBS in D2O (Cambridge Isotope Laboratories). D2O (0.7 mL) was again added to each petri dish and cells were gently scraped from the surface with a sterile cell scraper. A volume of 0.7 mL of the harvested cell suspension was transferred into a 5 mm NMR tube and 10 mL of 100 mM TMSP in D2O was added to each tube. Prior to NMR analysis, tubes were vortexed to ensure samples were in suspension. Control experiments using untreated cells were conducted in parallel with treated cells with the same incubation protocols and sample preparation. |
| Sampleprep Protocol Filename: | Prostate_Cells_Metabolomics_Procedure.doc |
| Sample Resuspension: | in deuterated water |
| Cell Type: | prostate |
Analysis:
| Analysis ID: | AN000216 |
| Laboratory Name: | Purdue Chemistry NMR Facility |
| Analysis Type: | NMR |
| Acquisition Date: | May 30, 2014; June 6, 2014 |
| Software Version: | AV-III-800 |
| Operator Name: | Dr. John Harwood |
| Detector Type: | TX1 |
| Chromatography ID: | CH000148 |
| Num Factors: | 4 |
| Num Metabolites: | 12 |
NMR:
| NMR ID: | NM000050 |
| Analysis ID: | AN000216 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 1.43 mM |
| Spectrometer Frequency: | 800 MHz |
| NMR Probe: | TX1, inverse |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5 mm x 7 in |
| Shimming Method: | gradient, topshim |
| Pulse Sequence: | zg one-pulse |
| Water Suppression: | presaturation |
| Pulse Width: | 8.5 msec |
| Power Level: | 12.25 W |
| Receiver Gain: | 912 |
| Offset Frequency: | 4.8 ppm |
| Presaturation Power Level: | 57 dB |
| Chemical Shift Ref Cpd: | TMSP |
| Temperature: | 295.9 |
| Number Of Scans: | 256 |
| Dummy Scans: | 8 |
| Acquisition Time: | 1.4680564 |
| Relaxation Delay: | 6.5 msec |
| Spectral Width: | 11160 Hz |
| Num Data Points Acquired: | 32 K |
| Real Data Points: | 32 K |
| Line Broadening: | 1 Hz |
| Zero Filling: | 16K |
| Apodization: | lorentzian |
| Baseline Correction Method: | polynomial |
| Chemical Shift Ref Std: | TMSP |
