Summary of Study ST001090
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 PR000729. The data can be accessed directly via it's Project DOI: 10.21228/M8FM38 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 | ST001090 |
| Study Title | NMR metabolomics study of Gemcitabine resistant cancer cells |
| Study Type | NMR metabolomics |
| Study Summary | 1D 1H NMR spectra were collected from the samples and analyzed using MVAPACK software (http://bionmr.unl.edu/mvapack.php). Multivariate analysis was conducted to study the metabolic phenotypes of the samples. |
| Institute | University of Nebraska-Lincoln |
| Department | Chemistry |
| Laboratory | Dr. Robert Powers and Pankaj Singh labs |
| Last Name | Gebregiworgis |
| First Name | Teklab |
| Address | 552 Hamilton Hall, 639 N. 12th Street, Lincoln, NE, 68588, USA |
| teklab@huskers.unl.edu | |
| Phone | (402) 472-3039 |
| Submit Date | 2018-09-25 |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2019-10-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000729 |
| Project DOI: | doi: 10.21228/M8FM38 |
| Project Title: | NMR metabolomics study of Gemcitabine resistant cancer cells |
| Project Type: | NMR metabolomics |
| Project Summary: | 1D 1H NMR based differential metabolomics study of T3M4 cells, which are gemcitabine sensitive, and gemcitabine resistant T3M4 cells (GemR) were cultured with or without gemcitabine treatment. 1D 1H NMR spectra were collected from the samples and analyzed using MVAPACK software (http://bionmr.unl.edu/mvapack.php). Using multivariate analysis, unique responses to gemcitabine treatment were revealed, which may be useful in the clinical setting for monitoring a patient’s therapeutic response. |
| Institute: | University of Nebraska-Lincoln |
| Department: | Chemistry |
| Laboratory: | Robert Powers and Pankaj Singh labs |
| Last Name: | Gebregiworgis |
| First Name: | Teklab |
| Address: | 552 Hamilton Hall, 639 N. 12th Street, Lincoln, NE, 68588, USA |
| Email: | teklab@huskers.unl.edu |
| Phone: | (402) 472-3039 |
| Funding Source: | NCI, NIGMS, AACR |
| Contributors: | Teklab Gebregiworgis, Fatema Bhinderwala, Vinee Purohit, Nina V. Chaika, Pankaj K. Singh, and Robert Powers |
Subject:
| Subject ID: | SU001134 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Biosource Or Supplier: | Gift from Dr. Michael Hollingsworth |
| Cell Strain Details: | T3M4 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Sensitivity |
|---|---|---|---|
| SA073598 | T3M4_25 | No | Resistant |
| SA073599 | T3M4_24 | No | Resistant |
| SA073600 | T3M4_22 | No | Resistant |
| SA073601 | T3M4_26 | No | Resistant |
| SA073602 | T3M4_23 | No | Resistant |
| SA073603 | T3M4_27 | No | Resistant |
| SA073604 | T3M4_30 | No | Resistant |
| SA073605 | T3M4_29 | No | Resistant |
| SA073606 | T3M4_28 | No | Resistant |
| SA073607 | T3M4_20 | No | Resistant |
| SA073608 | T3M4_21 | No | Resistant |
| SA073609 | T3M4_07 | No | Sensitive |
| SA073610 | T3M4_08 | No | Sensitive |
| SA073611 | T3M4_09 | No | Sensitive |
| SA073612 | T3M4_05 | No | Sensitive |
| SA073613 | T3M4_04 | No | Sensitive |
| SA073614 | T3M4_02 | No | Sensitive |
| SA073615 | T3M4_03 | No | Sensitive |
| SA073616 | T3M4_01 | No | Sensitive |
| SA073617 | T3M4_06 | No | Sensitive |
| SA073618 | T3M4_35 | Yes | Resistant |
| SA073619 | T3M4_34 | Yes | Resistant |
| SA073620 | T3M4_33 | Yes | Resistant |
| SA073621 | T3M4_36 | Yes | Resistant |
| SA073622 | T3M4_37 | Yes | Resistant |
| SA073623 | T3M4_40 | Yes | Resistant |
| SA073624 | T3M4_39 | Yes | Resistant |
| SA073625 | T3M4_38 | Yes | Resistant |
| SA073626 | T3M4_32 | Yes | Resistant |
| SA073627 | T3M4_31 | Yes | Resistant |
| SA073628 | T3M4_19 | Yes | Sensitive |
| SA073629 | T3M4_12 | Yes | Sensitive |
| SA073630 | T3M4_10 | Yes | Sensitive |
| SA073631 | T3M4_14 | Yes | Sensitive |
| SA073632 | T3M4_18 | Yes | Sensitive |
| SA073633 | T3M4_13 | Yes | Sensitive |
| SA073634 | T3M4_15 | Yes | Sensitive |
| SA073635 | T3M4_16 | Yes | Sensitive |
| SA073636 | T3M4_17 | Yes | Sensitive |
| SA073637 | T3M4_11 | Yes | Sensitive |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO001128 |
| Collection Summary: | For each of the cell culture, 1 x 106 cells were cultured and harvested at 70-80% confluence in a 100 mm Petri dish. The media was then removed by aspiration upon harvesting, and the cells were washed twice with PBS at pH 7.2. The cells were then lysed by the addition of 1 mL of an 80% methanol:water mixture at -80oC followed by incubation for 15 minutes in a -80oC freezer. The lysed cells were then transferred to a 1 ml Eppendorf tube using a cell scraper. The cell lysate was centrifuged at 16,200 g for 5 minutes and the supernatant was collected and transferred to a clean Eppendorf tube. 250 µL of nanopure water (Nanopure, Dubuque, IA) was added to the cell debris, the sample was mixed by pipetting, and then centrifuged as before. The two supernatants were combined, and the sample was dried by vacuum evaporation (SpeedVac® Plus, Savant, Thermo Scientific, Waltham, MA) followed by freeze-drying (Labconco, Kansas City, MO). |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001148 |
| Treatment Summary: | T3M4 wild type (WT) pancreatic cancer cells were cultured in DMEM with increasing concentrations of gemcitabine over a period of about 6 months. The resistance status of the cells at each gemcitabine dose was determined by calculating an IC50 using the MTT cytotoxicity assays. At the end of the 6-month treatment, the cell lines generated (GemR) were approximately 500-1000 fold resistant to gemcitabine as compared to the parental (WT) cells.Wild type T3M4 cells (WT), which are gemcitabine sensitive, and gemcitabine resistant T3M4 (GemR) were cultured with or without the addition of gemcitabine for the NMR metabolomics studies. A total of four cell culture groups were prepared that consisted of: (1) untreated T3M4 (WT) cells, (2) WT cells treated with 10 nM gemcitabine for a period of 12 hours (WT+), (3) untreated GemR cells, and (4) GemR cells treated with 10 nm gemcitabine for 12 hours (GemR+). |
Sample Preparation:
| Sampleprep ID: | SP001141 |
| Sampleprep Summary: | The dried metabolite extracts were reconstituted in 600 µL of 50 mM phosphate buffer in 99.8% D2O (Isotec, St. Louis, MO) at pH 7.2 (uncorrected). 50 µM of TMSP (3-(tetramethysilane) propionic acid-2,2,3,3-d4) were added for spectral referencing. The solution was mixed by gentle votexing and centrifuged at 13000 rpm for 5 min, and then the supernatant were transferred to 5 mm NMR tube. |
Analysis:
| Analysis ID: | AN001775 |
| Laboratory Name: | Dr. Robert Powers |
| Analysis Type: | NMR |
| Operator Name: | Teklab Gebregiworgis |
| Num Factors: | 4 |
NMR:
| NMR ID: | NM000133 |
| Analysis ID: | AN001775 |
| Instrument Name: | Bruker AVANCE DRX |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Spectrometer Frequency: | 500 MHz |
| Temperature: | 25 |
| Number Of Scans: | 128 |
| Dummy Scans: | 16 |
| Spectral Width: | 5483 Hz |
| Num Data Points Acquired: | 32000 |
