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.

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Study IDST000134
Study TitleMonitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy
Study TypeMetabolite level response after treatment with organoselenium
Study SummaryMetabolomics 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
DepartmentBiology/Chemistry
LaboratoryBiology/Chemistry
Last NameIsaac-Lam
First NameMeden
Address1401 S US Hwy 421, Westville, IN 46391
Emailisaaclam@pnc.edu
Phone219-785-5776
Submit Date2015-01-13
Num Groups6
Total Subjects18
Raw Data AvailableNo
Analysis Type DetailNMR
Release Date2015-01-13
Release Version1
Meden Isaac-Lam Meden Isaac-Lam
https://dx.doi.org/10.21228/M86C76
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA007395SeM (DU145)SeM DU145
SA007396SeM (PNT1A)SeM PNT1A
SA007397SeMSC (DU145)SeMSC DU145
SA007398SeMSC (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
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