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.
Study ID | ST003055 |
Study Title | Lipidomics analysis of the liver of THRB deficient (THRBKO) mice under normal chow conditions |
Study Type | Lipidomics |
Study Summary | Loss of THRB alters liver lipidome rhythms |
Institute | University of Luebeck |
Department | Bioanalytic Core facility |
Last Name | Inderhees |
First Name | Julica |
Address | Ratzeburger Allee 160, 23562 Luebeck |
julica.inderhees@uni-luebeck.de | |
Phone | +4945131012805 |
Submit Date | 2024-01-24 |
Num Groups | 12 |
Total Subjects | 36 |
Num Males | 36 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2024-08-14 |
Release Version | 1 |
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 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Genotype | Zeitgeber |
---|---|---|---|
SA331632 | 6 | d/d | 10 |
SA331633 | 17 | d/d | 10 |
SA331634 | 32 | d/d | 10 |
SA331635 | 30 | d/d | 14 |
SA331636 | 19 | d/d | 14 |
SA331637 | 8 | d/d | 14 |
SA331638 | 10 | d/d | 18 |
SA331639 | 28 | d/d | 18 |
SA331640 | 21 | d/d | 18 |
SA331641 | 2 | d/d | 2 |
SA331642 | 36 | d/d | 2 |
SA331643 | 13 | d/d | 2 |
SA331644 | 12 | d/d | 22 |
SA331645 | 23 | d/d | 22 |
SA331646 | 26 | d/d | 22 |
SA331647 | 15 | d/d | 6 |
SA331648 | 4 | d/d | 6 |
SA331649 | 34 | d/d | 6 |
SA331614 | 18 | +/d | 10 |
SA331615 | 5 | +/d | 10 |
SA331616 | 31 | +/d | 10 |
SA331617 | 20 | +/d | 14 |
SA331618 | 7 | +/d | 14 |
SA331619 | 29 | +/d | 14 |
SA331620 | 9 | +/d | 18 |
SA331621 | 27 | +/d | 18 |
SA331622 | 22 | +/d | 18 |
SA331623 | 1 | +/d | 2 |
SA331624 | 35 | +/d | 2 |
SA331625 | 14 | +/d | 2 |
SA331626 | 25 | +/d | 22 |
SA331627 | 24 | +/d | 22 |
SA331628 | 11 | +/d | 22 |
SA331629 | 33 | +/d | 6 |
SA331630 | 3 | +/d | 6 |
SA331631 | 16 | +/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 |