Summary of Study ST002276

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 PR001457. The data can be accessed directly via it's Project DOI: 10.21228/M8D133 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.

Show all samples | Perform analysis on untargeted data
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)

Study ID	ST002276
Study Title	Machine Learning Reveals Lipidome Dynamics in a Mouse Model of Ovarian Cancer
Study Summary	Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It presents little or no symptoms at the early stages, and typically unspecific symptoms at later stages. Of the OC subtypes, high-grade serous carcinoma (HGSC) is responsible for most OC deaths. However, very little is known about the metabolic course of this disease. In this longitudinal study, we investigated the temporal course of lipidome changes in a Dicer-Pten Double-Knockout (DKO) HGSC mouse model using machine and statistical learning approaches. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages were marked by more diverse lipids alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations provided evidence of perturbations in cell membrane stability, proliferation, and survival and candidates for early-stage and prognostic markers in humans.
Institute	Georgia Institute of Technology
Department	Chemistry and Biochemistry
Laboratory	Fernandez group
Last Name	Sah
First Name	Samyukta
Address	901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Email	ssah9@gatech.edu
Phone	5746780124
Submit Date	2022-09-01
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-09-28
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001457
Project DOI:	doi: 10.21228/M8D133
Project Title:	Machine Learning Reveals Lipidome Dynamics in a Mouse Model of Ovarian Cancer
Project Summary:	Ovarian cancer (OC) is one of the deadliest cancers affecting the female reproductive system. It presents little or no symptoms at the early stages, and typically unspecific symptoms at later stages. Of the OC subtypes, high-grade serous carcinoma (HGSC) is responsible for most OC deaths. However, very little is known about the metabolic course of this disease. In this longitudinal study, we investigated the temporal course of lipidome changes in a Dicer-Pten Double-Knockout (DKO) HGSC mouse model using machine and statistical learning approaches. Early progression of HGSC was marked by increased levels of phosphatidylcholines and phosphatidylethanolamines. In contrast, later stages were marked by more diverse lipids alterations, including fatty acids and their derivatives, triglycerides, ceramides, hexosylceramides, sphingomyelins, lysophosphatidylcholines, and phosphatidylinositols. These alterations provided evidence of perturbations in cell membrane stability, proliferation, and survival and candidates for early-stage and prognostic markers in humans.
Institute:	Georgia Institute of Technology
Department:	Chemistry and Biochemistry
Laboratory:	Fernandez group
Last Name:	Sah
First Name:	Samyukta
Address:	901 Atlantic Dr NW, Atlanta, GA, 30332, USA
Email:	ssah9@gatech.edu
Phone:	5746780124

Subject:

Subject ID:	SU002362
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	phenotype
SA218095	NC20_T7	control
SA218096	NC20_T6	control
SA218097	NC20_T5	control
SA218098	NC20_T8	control
SA218099	NC20_T11	control
SA218100	NC20_T4	control
SA218101	NC20_T10	control
SA218102	NC20_T9	control
SA218103	NC20_T3	control
SA218104	NC7_T13	control
SA218105	NC7_T14	control
SA218106	NC7_T12	control
SA218107	NC7_T11	control
SA218108	NC7_T9	control
SA218109	NC7_T10	control
SA218110	NC7_T15	control
SA218111	NC7_T16	control
SA218112	NC8_T1	control
SA218113	NC8_T2	control
SA218114	NC7_T19	control
SA218115	NC7_T18	control
SA218116	NC7_T17	control
SA218117	NC7_T8	control
SA218118	NC7_T7	control
SA218119	NC6_T17	control
SA218120	NC6_T18	control
SA218121	NC6_T16	control
SA218122	NC6_T15	control
SA218123	NC6_T14	control
SA218124	NC6_T19	control
SA218125	NC7_T1	control
SA218126	NC7_T5	control
SA218127	NC7_T6	control
SA218128	NC7_T4	control
SA218129	NC7_T3	control
SA218130	NC7_T2	control
SA218131	NC8_T3	control
SA218132	NC8_T4	control
SA218133	NC9_T9	control
SA218134	NC9_T10	control
SA218135	NC9_T8	control
SA218136	NC9_T7	control
SA218137	NC9_T5	control
SA218138	NC9_T6	control
SA218139	NC9_T11	control
SA218140	NC9_T12	control
SA218141	NC10_T2	control
SA218142	NC10_T3	control
SA218143	NC10_T1	control
SA218144	NC9_T15	control
SA218145	NC9_T13	control
SA218146	NC9_T4	control
SA218147	NC9_T3	control
SA218148	NC8_T8	control
SA218149	NC8_T9	control
SA218150	NC8_T7	control
SA218151	NC8_T6	control
SA218152	NC8_T5	control
SA218153	NC8_T10	control
SA218154	NC8_T11	control
SA218155	NC9_T1	control
SA218156	NC9_T2	control
SA218157	NC8_T15	control
SA218158	NC8_T13	control
SA218159	NC8_T12	control
SA218160	NC6_T13	control
SA218161	NC6_T12	control
SA218162	NC2_T7	control
SA218163	NC2_T8	control
SA218164	NC2_T6	control
SA218165	NC2_T5	control
SA218166	NC2_T3	control
SA218167	NC2_T4	control
SA218168	NC2_T9	control
SA218169	NC2_T10	control
SA218170	NC4_T1	control
SA218171	NC4_T2	control
SA218172	NC2_T13	control
SA218173	NC2_T12	control
SA218174	NC2_T11	control
SA218175	NC2_T2	control
SA218176	NC2_T1	control
SA218177	NC1_T5	control
SA218178	NC1_T6	control
SA218179	NC1_T4	control
SA218180	NC1_T3	control
SA218181	NC1_T2	control
SA218182	NC1_T7	control
SA218183	NC1_T8	control
SA218184	NC1_T12	control
SA218185	NC1_T13	control
SA218186	NC1_T11	control
SA218187	NC1_T10	control
SA218188	NC1_T9	control
SA218189	NC4_T3	control
SA218190	NC4_T4	control
SA218191	NC6_T3	control
SA218192	NC6_T4	control
SA218193	NC6_T2	control
SA218194	NC6_T1	control

Showing page 1 of 5 Results: 1 2 3 4 5 Next Showing results 1 to 100 of 459

Collection:

Collection ID:	CO002355
Collection Summary:	Serum samples were collected from Dicerflox/flox Ptenflox/flox Amhr2cre/+ (DKO) and Dicerflox/flox Ptenflox/flox without Amhr2cre/+ (Control) mice every two weeks until humane end point for sacrifice or development of ascites. Samples from 15 DKO mice (n = 231) and 15 control mice (n = 238) were used for lipidomics analyses.
Sample Type:	Blood (serum)

Treatment:

Treatment ID:	TR002374
Treatment Summary:	Dicerflox/flox Ptenflox/flox without Amhr2cre/+ (DKO Control mice) Dicerflox/flox Ptenflox/flox (DKO mice with high grade serous carcinoma )

Sample Preparation:

Sampleprep ID:	SP002368
Sampleprep Summary:	The lipid extraction solvent was prepared by adding 700 µL of the isotopically labeled lipid standard mixture to 42 mL of 2-propanol. Serum samples were thawed on ice, followed by extraction of non-polar metabolites. The extraction procedure was carried out by adding the prepared extraction solvent to 10-25 µL serum sample in a 3:1 ratio. Following this step, samples were vortex-mixed for 30 s and centrifuged at 13,000 rpm for 7 min. The resulting supernatant was transferred to LC vials and stored at -80 °C until analysis, which was performed within a week. A blank sample, prepared with LC-MS grade water, underwent the same sample preparation process as the serum samples. A pooled quality control (QC) sample was prepared by adding 2-5 µL aliquot of supernatant to each serum sample. This QC sample was analyzed every 10 runs to assess LC-MS instrument stability through the course of the experiment. Samples were run in a randomized order on consecutive days.

Sampleprep ID:

SP002368

Sampleprep Summary:

The lipid extraction solvent was prepared by adding 700 µL of the isotopically labeled lipid standard mixture to 42 mL of 2-propanol. Serum samples were thawed on ice, followed by extraction of non-polar metabolites. The extraction procedure was carried out by adding the prepared extraction solvent to 10-25 µL serum sample in a 3:1 ratio. Following this step, samples were vortex-mixed for 30 s and centrifuged at 13,000 rpm for 7 min. The resulting supernatant was transferred to LC vials and stored at -80 °C until analysis, which was performed within a week. A blank sample, prepared with LC-MS grade water, underwent the same sample preparation process as the serum samples. A pooled quality control (QC) sample was prepared by adding 2-5 µL aliquot of supernatant to each serum sample. This QC sample was analyzed every 10 runs to assess LC-MS instrument stability through the course of the experiment. Samples were run in a randomized order on consecutive days.

Combined analysis:

Analysis ID	AN003719	AN003720
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Accucore C30 (150 × 2.1mm,2.6um	Thermo Accucore C30 (150 × 2.1mm,2.6um
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Orbitrap ID-X Tribrid	Thermo Orbitrap ID-X Tribrid
Ion Mode	POSITIVE	NEGATIVE
Units	chromatographic peak area	chromatographic peak area

Chromatography:

Chromatography ID:	CH002755
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Accucore C30 (150 × 2.1mm,2.6um
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003468
Analysis ID:	AN003719
Instrument Name:	Thermo Orbitrap ID-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Spectral features (described as retention time, m/z pairs) were extracted with Compound Discoverer v3.2 (ThermoFisher Scientific) from the LC-MS datasets.
Ion Mode:	POSITIVE

MS ID:	MS003469
Analysis ID:	AN003720
Instrument Name:	Thermo Orbitrap ID-X Tribrid
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	spectral features (described as retention time, m/z pairs) were extracted with Compound Discoverer v3.2 (ThermoFisher Scientific) from the LC-MS datasets.
Ion Mode:	NEGATIVE