Summary of Study ST000454

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 PR000351. The data can be accessed directly via it's Project DOI: 10.21228/M8PC8X This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST000454
Study Title	Utilizing Metabolomics to Understand Novel Anti-Desmoid Tumor Drugs (part I)
Study Summary	This pilot study will use broad spectrum metabolomics to study the tumorigenesis process of fibroblasts to desmoids by investigating paired desmoid and fibroblast cell lines, in addition to unaffected fibroblast cells. Additionally, this pilot study will explore the effects of two of the active drugs identified on the desmoid and fibroblast cells.
Institute	RTI International
Last Name	Mercier
First Name	Kelly
Address	3040 E. Cornwallis Road
Email	kmercier@rti.org
Phone	919-541-6396
Submit Date	2016-08-31
Raw Data Available	Yes
Raw Data File Type(s)	1r
Analysis Type Detail	NMR
Release Date	2018-02-07
Release Version	1

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Project:

Project ID:	PR000351
Project DOI:	doi: 10.21228/M8PC8X
Project Title:	Utilizing Metabolomics to Understand Novel Anti-Desmoid Tumor Drugs
Project Summary:	Desmoid tumors (DT) are locally invasive soft tissue growths with no directed therapies currently. While two genes (β-catenin and adenomatous polyposis coli) have been found in patients who develop desmoids, it is unclear how these mutations and other downstream mechanisms lead to desmoid tumorigenesis. Extensive research has been explored in the molecular biology of desmoids; however, the use of metabolomics to understand the how the low molecular weight complements of cells, tissues, and biological fluids are perturbed by this highly localized disease. Additionally, the Desmoid Collaboration for a Cure has identified 45 active drugs against primary cell lines. It is unclear how these therapies perturb the metabolome, outside the Wnt and notch pathways.
Institute:	RTI International
Last Name:	Mercier
First Name:	Kelly
Address:	3040 E. Cornwallis Road
Email:	kmercier@rti.org
Phone:	919-541-6396

Subject:

Subject ID:	SU000475
Subject Type:	Human Cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Species Group:	Human

Factors:

Subject type: Human Cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Growth_type
SA023007	C_14_r2	Das.	Normal
SA023008	C_14_r3	Das.	Normal
SA023009	C_2_r2	Das.	Normal
SA023010	C_2_r3	Das.	Normal
SA023011	C_14_r1	Das.	Normal
SA023012	C_2_r1	Das.	Normal
SA023013	C_16_r2	Das.	Tumor
SA023014	C_4_r3	Das.	Tumor
SA023015	C_4_r2	Das.	Tumor
SA023016	C_4_r1	Das.	Tumor
SA023017	C_16_r1	Das.	Tumor
SA023018	C_16_r3	Das.	Tumor
SA023019	C_18_r1	Das.	Unaffected
SA023020	C_18_r4	Das.	Unaffected
SA023021	C_18_r6	Das.	Unaffected
SA022992	C_1_r5	DMSO	Normal
SA022993	C_13_r1	DMSO	Normal
SA022994	C_1_r6	DMSO	Normal
SA022995	C_13_r3	DMSO	Normal
SA022996	C_13_r2	DMSO	Normal
SA022997	C_1_r4	DMSO	Normal
SA022998	C_15_r1	DMSO	Tumor
SA022999	C_15_r3	DMSO	Tumor
SA023000	C_3_r1	DMSO	Tumor
SA023001	C_15_r2	DMSO	Tumor
SA023002	C_3_r3	DMSO	Tumor
SA023003	C_3_r2	DMSO	Tumor
SA023004	C_17_r6	DMSO	Unaffected
SA023005	C_17_r4	DMSO	Unaffected
SA023006	C_17_r5	DMSO	Unaffected
SA023022	C_11_r2	FAK Inh. 14	Normal
SA023023	C_5_r3	FAK Inh. 14	Normal
SA023024	C_11_r1	FAK Inh. 14	Normal
SA023025	C_5_r2	FAK Inh. 14	Normal
SA023026	C_11_r3	FAK Inh. 14	Normal
SA023027	C_5_r1	FAK Inh. 14	Normal
SA023028	C_6_r6	FAK Inh. 14	Tumor
SA023029	C_9_r2	FAK Inh. 14	Tumor
SA023030	C_6_r4	FAK Inh. 14	Tumor
SA023031	C_6_r5	FAK Inh. 14	Tumor
SA023032	C_9_r1	FAK Inh. 14	Tumor
SA023033	C_9_r3	FAK Inh. 14	Tumor
SA023034	C_19_r4	FAK Inh. 14	Unaffected
SA023035	C_19_r5	FAK Inh. 14	Unaffected
SA023036	C_19_r6	FAK Inh. 14	Unaffected
SA023037	C_12_r6	H2O	Normal
SA023038	C_12_r5	H2O	Normal
SA023039	C_12_r4	H2O	Normal
SA023040	C_7_r1	H2O	Normal
SA023041	C_7_r3	H2O	Normal
SA023042	C_7_r2	H2O	Normal
SA023043	C_10_r2	H2O	Tumor
SA023044	C_10_r1	H2O	Tumor
SA023045	C_10_r3	H2O	Tumor
SA023046	C_8_r1	H2O	Tumor
SA023047	C_8_r2	H2O	Tumor
SA023048	C_8_r3	H2O	Tumor
SA023049	C_20_r4	H2O	Unaffected
SA023050	C_20_r6	H2O	Unaffected
SA023051	C_20_r5	H2O	Unaffected
SA023052	CP_3_r2	Total Pool	Total Pool
SA023053	CP_3_r3	Total Pool	Total Pool
SA023054	CP_1_r2	Total Pool	Total Pool
SA023055	CP_3_r1	Total Pool	Total Pool
SA023056	CP_2_r6	Total Pool	Total Pool
SA023057	CP_2_r4	Total Pool	Total Pool
SA023058	CP_2_r5	Total Pool	Total Pool
SA023059	CP_1_r3	Total Pool	Total Pool
SA023060	CP_1_r1	Total Pool	Total Pool

Showing results 1 to 69 of 69

Showing results 1 to 69 of 69

Collection:

Collection ID:	CO000469
Collection Summary:	An aliquot of the media following treatment was collected, and the remainder of the media was aspirated. The cells were washed with PBS twice, and quenched with 8mL ice-cold isotonic 0.9% (w/v) saline for 2 minutes. Total cellular content was then extracted with 1.7mL ice-cold acetonitrile/water (50:50, v/v) solution. Cell extracts were collected using a cell scraper and quickly transferred to MagNA Lyser Green Beads tubes (Roche, Indianapolis, USA) and stored in -80°C. Media was added to empty plates and incubated together with the cells for the duration of the experiment served as a blank.
Sample Type:	Fibroblasts

Treatment:

Treatment ID:	TR000489
Treatment Summary:	Monolayer cell cultures of desmoid tumors and normal fibroblasts from desmoid patients and an unaffected fibroblast cell line were grown in DMEM supplemented with 5% fetal bovine serum and maintained at 37°C in 5% CO2. Cells were divided when confluent and experiments were performed between the third and sixth passages. Approximately 10 x 106 cells were treated with 1.0uM Dasatinib (Selleck, Houston, USA) dissolved in DMSO, or 0.5uM FAK Inhibitor 14 (Cayman Chemicals Company, Michigan, USA) dissolved in water. Cells were incubated in fresh media containing the inhibitors, or vehicle, for 24 hours.

Treatment ID:

TR000489

Treatment Summary:

Monolayer cell cultures of desmoid tumors and normal fibroblasts from desmoid patients and an unaffected fibroblast cell line were grown in DMEM supplemented with 5% fetal bovine serum and maintained at 37°C in 5% CO2. Cells were divided when confluent and experiments were performed between the third and sixth passages. Approximately 10 x 106 cells were treated with 1.0uM Dasatinib (Selleck, Houston, USA) dissolved in DMSO, or 0.5uM FAK Inhibitor 14 (Cayman Chemicals Company, Michigan, USA) dissolved in water. Cells were incubated in fresh media containing the inhibitors, or vehicle, for 24 hours.

Sample Preparation:

Sampleprep ID:	SP000482
Sampleprep Summary:	Cells were homogenized on the MagNA Lyzer, with two 30-sec cycles at 2000 rpm, resting in a -20 °C chilling block for 1 min in between pulses, and centrifuged samples at 16,000 rcf for 4 min. The cell lysate was transferred to a new 2 mL Lo-Bind Eppendorf tubes, with the final cell count approximately 10x10^6 cells for each sample. Of the twenty cell lysate samples, six samples had sufficient volume for study samples and to be included in an analytical quality control (QC) total pool. Aliquots from these cell lysate samples were combined, divided into three total pool aliquots, and processed identically to the cell lysate study samples. All study and pool samples were lyophilized to dryness and reconstituted in a 0.2M phosphate buffer, pH 7.4, in D2O with 10% Chenomx ISTD.

Sampleprep ID:

SP000482

Sampleprep Summary:

Cells were homogenized on the MagNA Lyzer, with two 30-sec cycles at 2000 rpm, resting in a -20 °C chilling block for 1 min in between pulses, and centrifuged samples at 16,000 rcf for 4 min. The cell lysate was transferred to a new 2 mL Lo-Bind Eppendorf tubes, with the final cell count approximately 10x10^6 cells for each sample. Of the twenty cell lysate samples, six samples had sufficient volume for study samples and to be included in an analytical quality control (QC) total pool. Aliquots from these cell lysate samples were combined, divided into three total pool aliquots, and processed identically to the cell lysate study samples. All study and pool samples were lyophilized to dryness and reconstituted in a 0.2M phosphate buffer, pH 7.4, in D2O with 10% Chenomx ISTD.

Analysis:

Analysis ID:	AN000711
Analysis Type:	NMR
Num Factors:	13

NMR:

NMR ID:	NM000078
Analysis ID:	AN000711
Instrument Name:	Bruker Avance III
Instrument Type:	FT-NMR
NMR Experiment Type:	1D 1H
Spectrometer Frequency:	700 MHz