Summary of Study ST002079

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 PR001319. The data can be accessed directly via it's Project DOI: 10.21228/M87125 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	ST002079
Study Title	Defining the mammalian coactivation of hepatic 12-hour clock and lipid metabolism
Study Summary	The 12-hour clock coordinates lipid homeostasis, energy metabolism and stress rhythms via the transcriptional regulator XBP1. However, the biochemical and physiological basis for integrated control of the 12-hour clock and diverse metabolic pathways remains unclear. Here, we show that steroid receptor coactivator SRC-3 coactivates XBP1 transcription and regulates hepatic 12-hour cistrome and gene rhythmicity. Mice lacking SRC-3 show abnormal 12-hour rhythms in hepatic transcription, metabolic functions, systemic energetics, and rate-limiting lipid metabolic processes including triglyceride, phospholipid and cardiolipin pathways. Notably, 12-hour clock coactivation is not only preserved, with its cistromic activation priming ahead of the zeitgeber cue of light, but concomitant with rhythmic remodeling in the absence of food. These findings reveal that SRC-3 integrates the mammalian 12-hour clock, energy metabolism, and membrane and lipid homeostasis, and demonstrates a role for the 12-hour clock machinery as an active transcriptional mechanism in anticipating physiological and metabolic energy needs and stresses.
Institute	Baylor College of Medicine
Last Name	Meng
First Name	Huan
Address	One Baylor Plaza BCM 130 Houston, TX 77030
Email	huanm@bcm.edu
Phone	5127729532
Submit Date	2022-02-04
Num Groups	12
Total Subjects	24
Num Males	24
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	Other
Release Date	2022-02-22
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001319
Project DOI:	doi: 10.21228/M87125
Project Title:	SRC-3 regulates the hepatic 12-hour lipidome
Project Summary:	To further define the 12-hour clock lipidome, we used a temporal lipidomics-based approach to identify hepatic lipid species in the mouse whole-liver. To unbiasedly characterize the 12-hour cycling lipidomes regulated by SRC-3, we profiled the temporal characteristics of oscillating lipidomes from adult male SRC-3 WT and KO littermates at 12-16 weeks of age under the same ZT condition (12h:12h LD cycle).
Institute:	Baylor College of Medicine
Last Name:	Meng
First Name:	Huan
Address:	One Baylor Plaza BCM 130, Houston, Texas, 77450, USA
Email:	huan.meng@gmail.com
Phone:	5127729532

Subject:

Subject ID:	SU002162
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Male

Factors:

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

mb_sample_id	local_sample_id	ZT_time	Genotype
SA196392	SRC-3 KO ZT0 replicate2 pos	ZT0	KO
SA196393	SRC-3 KO ZT0 replicate1 pos	ZT0	KO
SA196394	SRC-3 KO ZT0 replicate1 neg	ZT0	KO
SA196395	SRC-3 KO ZT0 replicate2 neg	ZT0	KO
SA196396	SRC-3 WT ZT0 replicate1 pos	ZT0	WT
SA196397	SRC-3 WT ZT0 replicate2 neg	ZT0	WT
SA196398	SRC-3 WT ZT0 replicate1 neg	ZT0	WT
SA196399	SRC-3 WT ZT0 replicate2 pos	ZT0	WT
SA196400	SRC-3 KO ZT12 replicate2 pos	ZT12	KO
SA196401	SRC-3 KO ZT12 replicate2 neg	ZT12	KO
SA196402	SRC-3 KO ZT12 replicate1 pos	ZT12	KO
SA196403	SRC-3 KO ZT12 replicate1 neg	ZT12	KO
SA196404	SRC-3 WT ZT12 replicate1 neg	ZT12	WT
SA196405	SRC-3 WT ZT12 replicate1 pos	ZT12	WT
SA196406	SRC-3 WT ZT12 replicate2 pos	ZT12	WT
SA196407	SRC-3 WT ZT12 replicate2 neg	ZT12	WT
SA196408	SRC-3 KO ZT16 replicate2 pos	ZT16	KO
SA196409	SRC-3 KO ZT16 replicate1 pos	ZT16	KO
SA196410	SRC-3 KO ZT16 replicate1 neg	ZT16	KO
SA196411	SRC-3 KO ZT16 replicate2 neg	ZT16	KO
SA196412	SRC-3 WT ZT16 replicate2 neg	ZT16	WT
SA196413	SRC-3 WT ZT16 replicate1 pos	ZT16	WT
SA196414	SRC-3 WT ZT16 replicate2 pos	ZT16	WT
SA196415	SRC-3 WT ZT16 replicate1 neg	ZT16	WT
SA196416	SRC-3 KO ZT20 replicate1 neg	ZT20	KO
SA196417	SRC-3 KO ZT20 replicate1 pos	ZT20	KO
SA196418	SRC-3 KO ZT20 replicate2 neg	ZT20	KO
SA196419	SRC-3 KO ZT20 replicate2 pos	ZT20	KO
SA196420	SRC-3 WT ZT20 replicate2 pos	ZT20	WT
SA196421	SRC-3 WT ZT20 replicate1 pos	ZT20	WT
SA196422	SRC-3 WT ZT20 replicate2 neg	ZT20	WT
SA196423	SRC-3 WT ZT20 replicate1 neg	ZT20	WT
SA196424	SRC-3 KO ZT4 replicate2 neg	ZT4	KO
SA196425	SRC-3 KO ZT4 replicate1 pos	ZT4	KO
SA196426	SRC-3 KO ZT4 replicate1 neg	ZT4	KO
SA196427	SRC-3 KO ZT4 replicate2 pos	ZT4	KO
SA196428	SRC-3 WT ZT4 replicate1 neg	ZT4	WT
SA196429	SRC-3 WT ZT4 replicate2 neg	ZT4	WT
SA196430	SRC-3 WT ZT4 replicate2 pos	ZT4	WT
SA196431	SRC-3 WT ZT4 replicate1 pos	ZT4	WT
SA196432	SRC-3 KO ZT8 replicate1 pos	ZT8	KO
SA196433	SRC-3 KO ZT8 replicate2 pos	ZT8	KO
SA196434	SRC-3 KO ZT8 replicate2 neg	ZT8	KO
SA196435	SRC-3 KO ZT8 replicate1 neg	ZT8	KO
SA196436	SRC-3 WT ZT8 replicate1 neg	ZT8	WT
SA196437	SRC-3 WT ZT8 replicate2 pos	ZT8	WT
SA196438	SRC-3 WT ZT8 replicate1 pos	ZT8	WT
SA196439	SRC-3 WT ZT8 replicate2 neg	ZT8	WT

Showing results 1 to 48 of 48

Showing results 1 to 48 of 48

Collection:

Collection ID:	CO002155
Collection Summary:	To further define the 12-hour clock lipidome, we used a temporal lipidomics-based approach to identify hepatic lipid species in the mouse whole-liver. To unbiasedly characterize the 12-hour cycling lipidomes regulated by SRC-3, we profiled the temporal characteristics of oscillating lipidomes from adult male SRC-3 WT and KO littermates at 12-16 weeks of age under the same ZT condition (12h:12h LD cycle). We then sampled two biological replicates of mouse liver tissues at a temporal resolution starting at ZT0 and proceeding every four hours for two complete 12-hour cycles to determine whether SRC-3 ablation perturbs the 12-hour clock lipidome.
Sample Type:	Liver

Treatment:

Treatment ID:	TR002174
Treatment Summary:	Mouse liver lipids were extracted using a modified Bligh-Dyer method. Briefly, 50 mg of crushed issue sample from mouse whole liver was used. A 2:2:2 volume ratio of water/methanol/dichloromethane was used for lipid extract at room temperature after spiking internal standards 17:0 LPC, 17:0PC, 17:0 PE, 17:0 PG, 17:0 ceramide, 17:0 SM, 17:0PS, 17:0PA, 17:0 TAG, 17:0MAG, DAG 16:0/18:1, CE 17:0. The organic layer was collected followed by a complete drying procedure under nitrogen.

Treatment ID:

TR002174

Treatment Summary:

Mouse liver lipids were extracted using a modified Bligh-Dyer method. Briefly, 50 mg of crushed issue sample from mouse whole liver was used. A 2:2:2 volume ratio of water/methanol/dichloromethane was used for lipid extract at room temperature after spiking internal standards 17:0 LPC, 17:0PC, 17:0 PE, 17:0 PG, 17:0 ceramide, 17:0 SM, 17:0PS, 17:0PA, 17:0 TAG, 17:0MAG, DAG 16:0/18:1, CE 17:0. The organic layer was collected followed by a complete drying procedure under nitrogen.

Sample Preparation:

Sampleprep ID:	SP002168
Sampleprep Summary:	Before MS analysis, the dried extract was resuspended in 100 ?L of Buffer B (10:5:85 Acetonitrile/water/Isopropyl alcohol) containing 10mM NH4OAc and subjected to LC/MS. The lipidome was separated using reverse-phase chromatography. High-performance Liquid Chromatography (LC) grade water, methanol, acetonitrile, dichloromethane, isopropanol from Fisher scientific were used per the manufacturer’s instructions. Mass spectrometry (MS) grade lipid standards from Avanti Polar Lipids (Alabaster, AL) and MS grade ammonium acetate from sigma Aldrich (St. Louis, MO) were used. For internal standards and quality controls, the lipid stock solution was prepared by weighing an exact amount of the lipid internal standards in Chloroform/Methanol/H2O, resulting in sample aliquots at concentration of 1mg/mL as stock solutions. The stock solutions were diluted to 100 pmol/?L by mixing an appropriate volume of the internal standards LPC 17:0/0:0, PG 17:0/17:0, PE 17:0/17:0, PC 17:0/17:0, TAG 17:0/17:0/17:0, SM 18:1/17:0, MAG 17:0, DAG 16:0/18:1, CE 17:0, ceramide d 18:1/17:0, PA 17:0, PI 17:0/20:4, and PS 17:0/17:0. To monitor instrument performance, 10 ?L of a dried matrix-free mixture of the internal standards was used, reconstituted in 100 ?L of buffer B (5% water, 85%Isopropanolol: 10%Acetonitrile in 10mM NH4OAc). To monitor the lipid extraction process, a standard pool representing the tissue sample aliquots was used.Shimadzu CTO-20A Nexera X2 UHPLC systems was used for data acquisition, equipped with a degasser, binary pump, thermostat-regulated auto sampler, and a column oven for chromatographic separation. For lipid separation, 5 uL of the lipid extract was injected to a 1.8 ?m particle 50 ? 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA). The column heater temperature was set at 55° C. For chromatographic elution, a linear gradient was used over a 20 min total run time, with 60% Solvent A (acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate) and 40% Solvent B (acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate) gradient in the first 10 minutes. The gradient was ramped in a linear fashion to 100% Solvent B for 7 minutes. Then the system was switched back to 60% Solvent B and 40% Solvent A for 3 minutes. A flow rate of 0.4 mL/min was used at an injection volume of 5?L. The column was equilibrated for 3 min and run at a flow rate of 0.4 mL/min for a total run time of 20 min. The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada).

Sampleprep ID:

SP002168

Sampleprep Summary:

Before MS analysis, the dried extract was resuspended in 100 ?L of Buffer B (10:5:85 Acetonitrile/water/Isopropyl alcohol) containing 10mM NH4OAc and subjected to LC/MS. The lipidome was separated using reverse-phase chromatography. High-performance Liquid Chromatography (LC) grade water, methanol, acetonitrile, dichloromethane, isopropanol from Fisher scientific were used per the manufacturer’s instructions. Mass spectrometry (MS) grade lipid standards from Avanti Polar Lipids (Alabaster, AL) and MS grade ammonium acetate from sigma Aldrich (St. Louis, MO) were used. For internal standards and quality controls, the lipid stock solution was prepared by weighing an exact amount of the lipid internal standards in Chloroform/Methanol/H2O, resulting in sample aliquots at concentration of 1mg/mL as stock solutions. The stock solutions were diluted to 100 pmol/?L by mixing an appropriate volume of the internal standards LPC 17:0/0:0, PG 17:0/17:0, PE 17:0/17:0, PC 17:0/17:0, TAG 17:0/17:0/17:0, SM 18:1/17:0, MAG 17:0, DAG 16:0/18:1, CE 17:0, ceramide d 18:1/17:0, PA 17:0, PI 17:0/20:4, and PS 17:0/17:0. To monitor instrument performance, 10 ?L of a dried matrix-free mixture of the internal standards was used, reconstituted in 100 ?L of buffer B (5% water, 85%Isopropanolol: 10%Acetonitrile in 10mM NH4OAc). To monitor the lipid extraction process, a standard pool representing the tissue sample aliquots was used.Shimadzu CTO-20A Nexera X2 UHPLC systems was used for data acquisition, equipped with a degasser, binary pump, thermostat-regulated auto sampler, and a column oven for chromatographic separation. For lipid separation, 5 uL of the lipid extract was injected to a 1.8 ?m particle 50 ? 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA). The column heater temperature was set at 55° C. For chromatographic elution, a linear gradient was used over a 20 min total run time, with 60% Solvent A (acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate) and 40% Solvent B (acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate) gradient in the first 10 minutes. The gradient was ramped in a linear fashion to 100% Solvent B for 7 minutes. Then the system was switched back to 60% Solvent B and 40% Solvent A for 3 minutes. A flow rate of 0.4 mL/min was used at an injection volume of 5?L. The column was equilibrated for 3 min and run at a flow rate of 0.4 mL/min for a total run time of 20 min. The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada).

Combined analysis:

Analysis ID	AN003391	AN003392
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Shimadzu CTO-20A Nexera X2 UHPLC systems	Shimadzu CTO-20A Nexera X2 UHPLC systems
Column	Waters Acquity BEH HSS T3 (50 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (50 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Triple TOF	Triple TOF
MS instrument name	ABI Sciex 5600+ TripleTOF	ABI Sciex 5600+ TripleTOF
Ion Mode	POSITIVE	NEGATIVE
Units	Normalized intensity	Normalized intensity

Chromatography:

Chromatography ID:	CH002507
Instrument Name:	Shimadzu CTO-20A Nexera X2 UHPLC systems
Column Name:	Waters Acquity BEH HSS T3 (50 x 2.1mm,1.8um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003158
Analysis ID:	AN003391
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
MS Comments:	The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada).
Ion Mode:	POSITIVE

MS ID:	MS003159
Analysis ID:	AN003392
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
MS Comments:	The data acquisition of each sample was performed in both positive and negative ionization modes using a TripleTOF 5600 equipped with a Turbo VTM ion source (AB Sciex, Concord, Canada).
Ion Mode:	NEGATIVE