Summary of Study ST003242
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 PR002013. The data can be accessed directly via it's Project DOI: 10.21228/M8DJ7S 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 | ST003242 |
| Study Title | Lipidomic analysis of kidney from Gclc WT and whole-body Gclc KO mice. |
| Study Summary | We found decreased triglycerides in the kidney of whole-body deletion of Gclc mice compared to wildtype mice. |
| Institute | University of Rochester Medical Center |
| Last Name | Harris |
| First Name | Isaac |
| Address | 601 Elmwood Ave, Rochester, New York, 14642-0001, USA |
| isaac_harris@urmc.rochester.edu | |
| Phone | 8572348624 |
| Submit Date | 2024-05-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002013 |
| Project DOI: | doi: 10.21228/M8DJ7S |
| Project Title: | Glutathione synthesis in the mouse liver supports lipid abundance through NRF2 repression. |
| Project Summary: | Cells rely on antioxidants to survive. The most abundant antioxidant is glutathione (GSH). The synthesis of GSH is non-redundantly controlled by the glutamate-cysteine ligase catalytic subunit (GCLC). GSH imbalance is implicated in many diseases, but the requirement for GSH in adult tissues is unclear. To interrogate this, we have developed a series of in vivo models to induce Gclc deletion in adult animals. We find that GSH is essential to lipid abundance in vivo. GSH levels are highest in liver tissue, which is also a hub for lipid production. While the loss of GSH does not cause liver failure, it decreases lipogenic enzyme expression, circulating triglyceride levels, and fat stores. Mechanistically, we find that GSH promotes lipid abundance by repressing NRF2, a transcription factor induced by oxidative stress. These studies identify GSH as a fulcrum in the liver's balance of redox buffering and triglyceride production. |
| Institute: | University of Rochester Medical Center |
| Last Name: | Harris |
| First Name: | Isaac |
| Address: | 601 Elmwood Ave, Rochester, New York, 14642-0001, USA |
| Email: | isaac_harris@urmc.rochester.edu |
| Phone: | 8572348624 |
Subject:
| Subject ID: | SU003361 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Male and female |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA353352 | Kidney_CreERT2_210 | kidney | Gclc KO |
| SA353353 | Kidney_CreERT2_232 | kidney | Gclc KO |
| SA353354 | Kidney_CreERT2_223 | kidney | Gclc KO |
| SA353355 | Kidney_CreERT2_216 | kidney | Gclc KO |
| SA353356 | Kidney_FF_226 | kidney | Gclc WT |
| SA353357 | Kidney_FF_218 | kidney | Gclc WT |
| SA353358 | Kidney_FF_219 | kidney | Gclc WT |
| SA353359 | Kidney_FF_225 | kidney | Gclc WT |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO003354 |
| Collection Summary: | Mice were euthanized with CO2 inhalation. Tissues were isolated, snap frozen on dry ice, and stored at -80C. |
| Sample Type: | Kidney |
Treatment:
| Treatment ID: | TR003370 |
| Treatment Summary: | Gclc WT (Gclc f/f) and whole-body Gclc KO (Gclc f/f Rosa26-CreERT2) were treated with 160 mg/kg i.p. injection of tamoxifen daily for five consecutive days. After approximately 14 days, mice were euthanized and tissue was isolated and stored. |
Sample Preparation:
| Sampleprep ID: | SP003368 |
| Sampleprep Summary: | Tissues were homogenized with a pre-chilled BioPulverizer (59012MS, BioSpec) and then placed on dry ice. The chloroform:methanol extraction solvent (v:v = 1:1) was added to the homogenate to meet 50 mg/mL. The samples were then sonicated in ice-cold water using BiorupterTM UCD-200 sonicator for 5 min (30 s sonication and 30 s rest cycle; high voltage mode). The lipid extracts were cleared by centrifugation (17,000g, 20°C, 10 min), and the lipids in the supernatant were analyzed by LC-MS. |
Combined analysis:
| Analysis ID | AN005311 | AN005312 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Perkin Elmer Brownlee SPP C18 (75 × 2.1mm, 2.7um) | Perkin Elmer Brownlee SPP C18 (75 × 2.1mm, 2.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Normalized to the median value of total lipid signals | Normalized to the median value of total lipid signals |
Chromatography:
| Chromatography ID: | CH004016 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Perkin Elmer Brownlee SPP C18 (75 × 2.1mm, 2.7um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0–2 min 35% B, 2–8 min from 35 to 80% B, 8–22 min from 80 to 99% B, 22–36 min 99% B, and 36.1–40 min from 99 to 35% B. |
| Flow Rate: | 0.400 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10mM ammonium acetate |
| Solvent B: | 50% acetonitrile/50% isopropanol; 0.1% formic acid; 10mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005041 |
| Analysis ID: | AN005311 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For the mass spectrometry, the data-dependent MS2 scan conditions were applied in both positive and negative mode: the scan range was from m/z 250–1500, resolution was 60,000 for MS, and 30,000 for DDMS2 (top 10), and the AGC target was 3E6 for full MS and 1E5 for DDMS2, allowing ions to accumulate for up to 200 ms for MS and 50 ms for MS/MS. For MS/MS, the following settings are used: isolation window width 1.2 m/z with an offset of 0.5 m/z, stepped NCE at 10, 15, and 25 a.u., minimum AGC 5E2, and dynamic exclusion of previously sampled peaks for 8 s. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005042 |
| Analysis ID: | AN005312 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For the mass spectrometry, the data-dependent MS2 scan conditions were applied in both positive and negative mode: the scan range was from m/z 250–1500, resolution was 60,000 for MS, and 30,000 for DDMS2 (top 10), and the AGC target was 3E6 for full MS and 1E5 for DDMS2, allowing ions to accumulate for up to 200 ms for MS and 50 ms for MS/MS. For MS/MS, the following settings are used: isolation window width 1.2 m/z with an offset of 0.5 m/z, stepped NCE at 10, 15, and 25 a.u., minimum AGC 5E2, and dynamic exclusion of previously sampled peaks for 8 s. |
| Ion Mode: | NEGATIVE |
