Summary of Study ST001312

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 PR000890. The data can be accessed directly via it's Project DOI: 10.21228/M8ND7K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST001312
Study Title	Lipid expression in serum after early lifer exposure to an endocrine disruptor at 70 days postnatal (part-III)
Study Type	Lipid expression after chemical exposure versus control.
Study Summary	Our early-life environment has a profound influence on developing organs that impact metabolic function and determines disease susceptibility across the life-course. Using a rat model for exposure to an endocrine disrupting chemical (EDC), we show that early-life exposure causes metabolic dysfunction in adulthood and reprograms histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature. This epigenomic reprogramming persists long after the initial exposure, but many reprogrammed genes remain transcriptionally silent with their impact on metabolism not revealed until a later life exposure to a Western-style diet. Diet-dependent metabolic disruption was largely driven by reprogramming of the Early Growth Response 1 (EGR1) transcriptome and production of metabolites in pathways linked to cholesterol, lipid and one-carbon metabolism. These findings demonstrate the importance of epigenome:environment interactions, which early in life accelerate epigenomic aging, and later in adulthood unlock metabolically restricted epigenetic reprogramming to drive metabolic dysfunction.
Institute	Baylor College of Medicine
Last Name	Walker
First Name	Cheryl
Address	1 Baylor Plaza
Email	Cheryl.walker@bcm.edu
Phone	7137988219
Submit Date	2020-01-24
Num Groups	2
Total Subjects	10
Num Males	10
Analysis Type Detail	LC-MS
Release Date	2020-03-11
Release Version	1

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Combined analysis:

Analysis ID	AN002184	AN002185
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Shimadzu Nexera-x2	Shimadzu Nexera-x2
Column	Acquity HSS UPLC T3 (50 x 2.1mm,1.8um)	1.8 μm particle 50 × 2.1 mm
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	ABI Sciex 5600 TripleTOF	ABI Sciex 5600 TripleTOF
Ion Mode	POSITIVE	NEGATIVE
Units	peak intensity	peak intensity

MS:

MS ID:	MS002031
Analysis ID:	AN002184
Instrument Name:	ABI Sciex 5600 TripleTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For data acquisition through LC/MS analysis, we used a Shimadzu CTO-20A Nexera X2 UHPLC system equipped with a degasser, binary pump, thermostatted auto sampler, and a column oven for chromatographic separation. The column heater temperature was set at 55°C. For lipid separation, the 5 uL of the lipid extract was injected into a 1.8 μm particle 50 × 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA) which heats to 55°C. Acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate was solvent A and acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate was solvent B. For chromatographic elution we used a linear gradient over a 20 min total run time, with 60% solvent A and 40% solvent B gradient in the first 10 minutes, then the gradient was ramped in a linear fashion to 100% solvent B which was maintained for 7 minutes. After that the system was switched back to 60% solvent B and 40% solvent A for 3 minutes. The flow rate used for these experiments was 0.4 mL/min and the injection volume was 5μL. The column was equilibrated for 3 min before the next injection 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). The column effluent was directed to the electrospray ionization source. The voltage of source was set to 5500 V for positive ionization and 4500 V for negative ionization mode, the declustering potential was set to 60 V, and the source temperature to 450oC for both modes. The curtain gas flow, nebulizer, and heater gas were set to 30, 40, and 45 units, respectively. The instrument performed one TOF MS survey scan (150 ms) and 15 MS/MS scans with a total duty cycle time of 2.4 s. The mass range in both modes was 50-1200 m/z. We controlled the acquisition of MS/MS spectra by data-dependent acquisition (DDA) function of the Analyst TF software (AB Sciex, Concord, Canada) with the following parameters: dynamic background subtraction, charge monitoring to exclude multiply charged ions and isotopes, and dynamic exclusion of former target ions for 9 s. Rolling collision energy spread was set whereby the software calculated the collision energy value to be applied as a function of m/z. Mass accuracy was maintained by the use of an automated calibrant delivery system interfaced to the second inlet of the DuoSpray source.
Ion Mode:	POSITIVE

MS ID:	MS002032
Analysis ID:	AN002185
Instrument Name:	ABI Sciex 5600 TripleTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For data acquisition through LC/MS analysis, we used a Shimadzu CTO-20A Nexera X2 UHPLC system equipped with a degasser, binary pump, thermostatted auto sampler, and a column oven for chromatographic separation. The column heater temperature was set at 55°C. For lipid separation, the 5 uL of the lipid extract was injected into a 1.8 μm particle 50 × 2.1 mm Acquity HSS UPLC T3 column (Waters, Milford, MA) which heats to 55°C. Acetonitrile/water (40:60, v/v) with 10 mM ammonium acetate was solvent A and acetonitrile/water/isopropanol (10:5:85 v/v) with 10 mM ammonium acetate was solvent B. For chromatographic elution we used a linear gradient over a 20 min total run time, with 60% solvent A and 40% solvent B gradient in the first 10 minutes, then the gradient was ramped in a linear fashion to 100% solvent B which was maintained for 7 minutes. After that the system was switched back to 60% solvent B and 40% solvent A for 3 minutes. The flow rate used for these experiments was 0.4 mL/min and the injection volume was 5μL. The column was equilibrated for 3 min before the next injection 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). The column effluent was directed to the electrospray ionization source. The voltage of source was set to 5500 V for positive ionization and 4500 V for negative ionization mode, the declustering potential was set to 60 V, and the source temperature to 450oC for both modes. The curtain gas flow, nebulizer, and heater gas were set to 30, 40, and 45 units, respectively. The instrument performed one TOF MS survey scan (150 ms) and 15 MS/MS scans with a total duty cycle time of 2.4 s. The mass range in both modes was 50-1200 m/z. We controlled the acquisition of MS/MS spectra by data-dependent acquisition (DDA) function of the Analyst TF software (AB Sciex, Concord, Canada) with the following parameters: dynamic background subtraction, charge monitoring to exclude multiply charged ions and isotopes, and dynamic exclusion of former target ions for 9 s. Rolling collision energy spread was set whereby the software calculated the collision energy value to be applied as a function of m/z. Mass accuracy was maintained by the use of an automated calibrant delivery system interfaced to the second inlet of the DuoSpray source.
Ion Mode:	NEGATIVE