Summary of Study ST002914

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 PR001812. The data can be accessed directly via it's Project DOI: 10.21228/M8GX42 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	ST002914
Study Title	Untangling the Dynamics of Lysine Acetylation and Phosphorylation in Adipogenesis in the Established Human and Mouse Adipocyte Cell Lines SGBS and 3T3L1
Study Summary	Obesity is one of the most pressing global public health challenges of our time with yet increasing prevalence. Characterized by enlarged and dysfunctional adipose tissue, it is often associated with the development of metabolic or cardiovascular comorbidities. A sound understanding of the processes underlying adipogenesis, the differentiation of a preadipocyte into a mature and lipid laden adipocyte, provide the basic knowledge for future research on the causes and consequences of obesity. The tricarboxylic acid cycle represents the central metabolic hub, that provides energy equivalents, metabolic building blocks and critical intermediates such as acetyl-CoA as precursor for protein acetylation and de novo lipogenesis. Stable cell lines are an integral part of research into the development and physiology of adipocytes in health and disease and various models have been used to date. In this study we demonstrated the vivid temporal dynamics of central carbon metabolites during the differentiation of SGBS and 3T3-L1 adipocytes. Detected metabolite levels showed distinct temporal profiles, partly with cell-line specificities.
Institute	Helmholtz Centre for Environmental Research
Department	Molecular Systems Biology
Last Name	Engelmann
First Name	Beatrice
Address	Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email	beatrice.engelmann@ufz.de
Phone	00493412351099
Submit Date	2023-09-26
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2023-10-27
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001812
Project DOI:	doi: 10.21228/M8GX42
Project Title:	Untangling the Dynamics of Lysine Acetylation and Phosphorylation in Adipogenesis in the Established Human and Mouse Adipocyte Cell Lines SGBS and 3T3L1
Project Summary:	Obesity is one of the most pressing global public health challenges of our time with yet increasing prevalence. Characterized by enlarged and dysfunctional adipose tissue, it is often associated with the development of metabolic or cardiovascular comorbidities. A sound understanding of the processes underlying adipogenesis, the differentiation of a preadipocyte into a mature and lipid-laden adipocyte, provide the basic knowledge for future research on the causes and consequences of obesity. The tricarboxylic acid cycle represents the central metabolic hub, that provides energy equivalents, metabolic building blocks and critical intermediates such as acetyl-CoA as precursor for protein acetylation and de novo lipogenesis. Stable cell lines are an integral part of research into the development and physiology of adipocytes in health and disease and various models have been used to date. In this study we demonstrated the vivid temporal dynamics of central carbon metabolites during the differentiation of SGBS and 3T3-L1 adipocytes. Detected metabolite levels showed distinct temporal profiles, partly with cell-line specificities.
Institute:	Helmholtz Centre for Environmental Research
Department:	Molecular Systems Biology
Last Name:	Engelmann
First Name:	Beatrice
Address:	Permoserstraße 15, Leipzipg, Saxony, 03418, Germany
Email:	beatrice.engelmann@ufz.de
Phone:	00493412351099

Subject:

Subject ID:	SU003027
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Replicate	Species
SA316365	SGBS_ctrl_d0_1	d0	1	Homo sapiens
SA316366	3T3L1_ctrl_d0_1	d0	1	Mus musculus
SA316367	SGBS_ctrl_d0_2	d0	2	Homo sapiens
SA316368	3T3L1_ctrl_d0_2	d0	2	Mus musculus
SA316369	SGBS_ctrl_d0_3	d0	3	Homo sapiens
SA316370	3T3L1_ctrl_d0_3	d0	3	Mus musculus
SA316371	SGBS_ctrl_d0_4	d0	4	Homo sapiens
SA316372	3T3L1_ctrl_d0_4	d0	4	Mus musculus
SA316373	SGBS_ctrl_d0_5	d0	5	Homo sapiens
SA316374	3T3L1_ctrl_d0_5	d0	5	Mus musculus
SA316375	SGBS_ctrl_d0_6	d0	6	Homo sapiens
SA316376	3T3L1_ctrl_d0_6	d0	6	Mus musculus
SA316377	SGBS_ctrl_d12_1	d12	1	Homo sapiens
SA316378	SGBS_ctrl_d12_2	d12	2	Homo sapiens
SA316379	SGBS_ctrl_d12_3	d12	3	Homo sapiens
SA316380	SGBS_ctrl_d12_4	d12	4	Homo sapiens
SA316381	SGBS_ctrl_d12_5	d12	5	Homo sapiens
SA316382	SGBS_ctrl_d12_6	d12	6	Homo sapiens
SA316383	3T3L1_ctrl_d10_1	d1	1	Mus musculus
SA316384	3T3L1_ctrl_d10_2	d1	2	Mus musculus
SA316385	3T3L1_ctrl_d10_3	d1	3	Mus musculus
SA316386	3T3L1_ctrl_d10_4	d1	4	Mus musculus
SA316387	3T3L1_ctrl_d10_5	d1	5	Mus musculus
SA316388	3T3L1_ctrl_d10_6	d1	6	Mus musculus
SA316389	SGBS_ctrl_d3_1	d3	1	Homo sapiens
SA316390	3T3L1_ctrl_d3_1	d3	1	Mus musculus
SA316391	SGBS_ctrl_d3_2	d3	2	Homo sapiens
SA316392	3T3L1_ctrl_d3_2	d3	2	Mus musculus
SA316393	SGBS_ctrl_d3_3	d3	3	Homo sapiens
SA316394	3T3L1_ctrl_d3_3	d3	3	Mus musculus
SA316395	SGBS_ctrl_d3_4	d3	4	Homo sapiens
SA316396	3T3L1_ctrl_d3_4	d3	4	Mus musculus
SA316397	SGBS_ctrl_d3_5	d3	5	Homo sapiens
SA316398	3T3L1_ctrl_d3_5	d3	5	Mus musculus
SA316399	SGBS_ctrl_d3_6	d3	6	Homo sapiens
SA316400	3T3L1_ctrl_d3_6	d3	6	Mus musculus
SA316401	3T3L1_ctrl_d5_1	d5	1	Mus musculus
SA316402	3T3L1_ctrl_d5_2	d5	2	Mus musculus
SA316403	3T3L1_ctrl_d5_3	d5	3	Mus musculus
SA316404	3T3L1_ctrl_d5_4	d5	4	Mus musculus
SA316405	3T3L1_ctrl_d5_5	d5	5	Mus musculus
SA316406	3T3L1_ctrl_d5_6	d5	6	Mus musculus
SA316407	SGBS_ctrl_d6_1	d6	1	Homo sapiens
SA316408	SGBS_ctrl_d6_2	d6	2	Homo sapiens
SA316409	SGBS_ctrl_d6_3	d6	3	Homo sapiens
SA316410	SGBS_ctrl_d6_4	d6	4	Homo sapiens
SA316411	SGBS_ctrl_d6_5	d6	5	Homo sapiens
SA316412	SGBS_ctrl_d6_6	d6	6	Homo sapiens
SA316413	3T3L1_ctrl_d7_1	d7	1	Mus musculus
SA316414	3T3L1_ctrl_d7_2	d7	2	Mus musculus
SA316415	3T3L1_ctrl_d7_3	d7	3	Mus musculus
SA316416	3T3L1_ctrl_d7_4	d7	4	Mus musculus
SA316417	3T3L1_ctrl_d7_5	d7	5	Mus musculus
SA316418	3T3L1_ctrl_d7_6	d7	6	Mus musculus
SA316419	SGBS_ctrl_d9_1	d9	1	Homo sapiens
SA316420	SGBS_ctrl_d9_2	d9	2	Homo sapiens
SA316421	SGBS_ctrl_d9_3	d9	3	Homo sapiens
SA316422	SGBS_ctrl_d9_4	d9	4	Homo sapiens
SA316423	SGBS_ctrl_d9_5	d9	5	Homo sapiens
SA316424	SGBS_ctrl_d9_6	d9	6	Homo sapiens

Showing results 1 to 60 of 60

Showing results 1 to 60 of 60

Collection:

Collection ID:	CO003020
Collection Summary:	Human SGBS cells were provided by the laboratory of Prof. Dr. Wabitsch at the University Clinic Ulm. Cells were differentiated according to the standard protocol described previously (Wabitsch et al., 2001). 3T3-L1 mouse embryonic fibroblasts were purchased from the American Type Culture Collection (ATCC, CL-173, USA).
Sample Type:	Adipose tissue
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003036
Treatment Summary:	Both cell lines were maintained under 5% CO2 at 37°C and 95% humidity. Cell culture experiments for metabolomic (SGBS and 3T3L1) data analysis were performed in 6 replicates. Cells were cultivated until day0,day6 and day12 for the SGBS cell line, and until day0, day5 and day10 for the 3T3-L1 cells.

Sample Preparation:

Sampleprep ID:	SP003033
Sampleprep Summary:	Intracellular metabolites were extracted using a 1:1:1 methanol:water:chloroform extraction protocol. Briefly, culture media was removed and cells were rinsed with icecold 0.9 % sodium chloride solution. The rinsing solution was removed and the cells metabolism was quenched by adding equal volumes of methanol, followed by icecold deionized water. Cells were scraped off the culture plate and combined chloroform. Samples were vortexed and kept on a shaker at 4°C for 20 min at 1400 rpm. Cell debris was removed by centrifugation. A fixed volume of the polar upper phase was transferred to new tubes and dried to completeness.

Sampleprep ID:

SP003033

Sampleprep Summary:

Intracellular metabolites were extracted using a 1:1:1 methanol:water:chloroform extraction protocol. Briefly, culture media was removed and cells were rinsed with icecold 0.9 % sodium chloride solution. The rinsing solution was removed and the cells metabolism was quenched by adding equal volumes of methanol, followed by icecold deionized water. Cells were scraped off the culture plate and combined chloroform. Samples were vortexed and kept on a shaker at 4°C for 20 min at 1400 rpm. Cell debris was removed by centrifugation. A fixed volume of the polar upper phase was transferred to new tubes and dried to completeness.

Combined analysis:

Analysis ID	AN004784
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Agilent 1290 Infinity II
Column	Waters XSelect XP HSS T3 (150 x 2.1mm, 2.5um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	ABI Sciex 6500+
Ion Mode	NEGATIVE
Units	AUC

Chromatography:

Chromatography ID:	CH003615
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Waters XSelect XP HSS T3 (150 x 2.1mm, 2.5um)
Column Temperature:	40
Flow Gradient:	0-5 min 0% B, 5-9 min 0%- 2% B, 9-9.5 min 2-6% B, 9.5-11.5 min 6% B, 11.5-12 min 6-11% B, 12-13.5 min 11% B, 13.5-15.5 min 11-28% B, 15.5-16.5 min 28-53% B, 16.5-22.5 53% B, 22.5-23 min 53-0% B, 23-33 min 0% B
Flow Rate:	0-15.5 min 0.4 mL/min, 15.5-16.5 min 0.4-0.15 mL/min, 16.5-23 min 0.15 mL/min, 23-27 min 0.15-0.4 mL/min, 27-33 min 0.4 mL/min
Solvent A:	10mM TBA, 10mM acetic acid, 5% MeOH, 2% IPA in water
Solvent B:	100% IPA
Chromatography Type:	Reversed phase

MS:

MS ID:	MS004530
Analysis ID:	AN004784
Instrument Name:	ABI Sciex 6500+
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	For identification and quantitation, a scheduled MRM method was used, with specific transitions for every metabolite. Data acquisition and peak integration were performed in Analyst® software (Version 1.7.1).
Ion Mode:	NEGATIVE