Summary of Study ST003055

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 PR001904. The data can be accessed directly via it's Project DOI: 10.21228/M8M718 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.

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Study IDST003055
Study TitleLipidomics analysis of the liver of THRB deficient (THRBKO) mice under normal chow conditions
Study TypeLipidomics
Study SummaryLoss of THRB alters liver lipidome rhythms
Institute
University of Luebeck
DepartmentBioanalytic Core facility
Last NameInderhees
First NameJulica
AddressRatzeburger Allee 160, 23562 Luebeck
Emailjulica.inderhees@uni-luebeck.de
Phone+4945131012805
Submit Date2024-01-24
Num Groups12
Total Subjects36
Num Males36
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-08-14
Release Version1
Julica Inderhees Julica Inderhees
https://dx.doi.org/10.21228/M8M718
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001904
Project DOI:doi: 10.21228/M8M718
Project Title:Thyroid hormone receptor beta (THRB) dependent regulation of diurnal hepatic lipid metabolism in adult male mice
Project Type:Lipidomics
Project Summary:Thyroid hormones (THs) are critical regulators of systemic energy metabolism and homeostasis. In the liver, high TH action protects against steatosis by enhancing cholesterol and triglyceride turnover, with thyroid hormone receptor beta (THRB) signaling playing a pivotal role. This study probed the potential interaction between THRB action and another critical regulator of liver energy metabolism, the circadian clock. Liver transcriptome analysis of THRB deficient (THRBKO) mice under normal chow conditions revealed a markedly modest impact of THRB deletion. Temporal transcriptome and lipidome profiling uncovered significant alterations in diurnal metabolic rhythms attributable to THRB deficiency pointing to a pro-steatotic state with elevated levels of cholesterol, tri- and diacylglycerides, and fatty acids. These findings were confirmed by THRB agonization in hepatocytes under steatosis-promoting conditions in vitro.
Institute:University of Luebeck
Department:Bioanalytic Core facility
Last Name:Inderhees
First Name:Julica
Address:Ratzburger Allee 160, Luebeck, Schleswig-Holstein, 23562, Germany
Email:julica.inderhees@uni-luebeck.de
Phone:+4945131012805
Contributors:Leonardo Vinicius Monteiro de Assis, Julica Inderhees

Subject:

Subject ID:SU003170
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:wild type (THRB+/-) and knockout (THRB-/-)
Age Or Age Range:2-3 months
Gender:Male
Animal Housing:Standard conditions
Animal Light Cycle:12 hour light/dark cycle
Animal Feed:normal chow, 5 % fat, 1314, Altromin, Germany
Animal Water:ad libitum
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Genotype Zeitgeber
SA3316326d/d 10
SA33163317d/d 10
SA33163432d/d 10
SA33163530d/d 14
SA33163619d/d 14
SA3316378d/d 14
SA33163810d/d 18
SA33163928d/d 18
SA33164021d/d 18
SA3316412d/d 2
SA33164236d/d 2
SA33164313d/d 2
SA33164412d/d 22
SA33164523d/d 22
SA33164626d/d 22
SA33164715d/d 6
SA3316484d/d 6
SA33164934d/d 6
SA33161418+/d 10
SA3316155+/d 10
SA33161631+/d 10
SA33161720+/d 14
SA3316187+/d 14
SA33161929+/d 14
SA3316209+/d 18
SA33162127+/d 18
SA33162222+/d 18
SA3316231+/d 2
SA33162435+/d 2
SA33162514+/d 2
SA33162625+/d 22
SA33162724+/d 22
SA33162811+/d 22
SA33162933+/d 6
SA3316303+/d 6
SA33163116+/d 6
Showing results 1 to 36 of 36

Collection:

Collection ID:CO003163
Collection Summary:Mice were culled by cervical dislocation at 4-hour intervals, tissues were kept in dry ice, and stored at -80°C. Zirconium oxide beats and 500 µl of water were added to the frozen tissue (70 – 150 mg). Liver samples were homogenized for 3 min at speed level 8 (Bullet Blender, Next Advance, New Yourk, USA) and centrifuged (2,000 g/10 min/4 °C). The supernatant (400 µl) was transferred into a new reaction tube and diluted accordingly to reach a protein concentration between 0.6 mg/ml and 1.2 mg/ml.
Sample Type:Liver
Collection Frequency:4 hours
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003179
Treatment Summary:wild type (THRB+/-) and knockout (THRB-/-) Collection of samples at a specific "Zeitgeber" time [hours] to investigate circadian rhythms.

Sample Preparation:

Sampleprep ID:SP003176
Sampleprep Summary:Lipids were extracted by adding 1 ml of methanol/methyl tertiary-butyl ether/chloroform (1.33:1:1, v/v), containing butylated hydroxytoluene (100 mg/L, Sigma-Aldrich, Germany) and 2.5 ml/L of SPLASH internal standard mix (Avanti Polar Lipids, Alabaster, USA), to 50 µl of tissue homogenate. After incubation and centrifugation, supernatants were dried under vacuum and resuspended in 50 µl of methanol/isopropyl alcohol (1:1, v/v) for LC-MS/MS analysis.
Extract Storage:4℃

Combined analysis:

Analysis ID AN005009
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 RS
Column Thermo Accucore C30 (150 x 2.1mm,2.6um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units relative area

Chromatography:

Chromatography ID:CH003783
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Thermo Accucore C30 (150 x 2.1mm,2.6um)
Column Temperature:45°C
Flow Gradient:Gradient elution: from 30 – 43 % B in 2.0 min, 43 – 55 % B in 0.1 min, to 65 % B in 9.9 min, to 85 % B in 6 min and to 100 % B in 2 min. An isocratic step of 100 % B was held for 15 min and returned to initial conditions in 0.1 min and held for 2.9 min
Flow Rate:0.26ml/min
Solvent A:acetonitril/water (6:4); 10mM ammonium acetate; 0.1% formic acid
Solvent B:isopropanol/acetonitril (9:1); 10mM ammonium acetate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004748
Analysis ID:AN005009
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition with data-dependent MS2 scans (top 15) was performed in positive and negative ionization mode via polarity switching. Lipids were identified based on exact mass, retention time, fragmentation spectra and isotopic pattern. Compound Discoverer 3.3 was used for data processing.
Ion Mode:UNSPECIFIED
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