Summary of Study ST002396
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 PR001543. The data can be accessed directly via it's Project DOI: 10.21228/M87T4V 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 | ST002396 |
| Study Title | p53 K316P mutation results in increased liver triglyceride levels and increased rates of de novo lipogenesis. |
| Study Summary | Our lab generated the p53 K316P mouse, which mimicks a common amino acid change found in bats. The K316P mutation, found in the nuclear localization signal of p53, results in increased cytoplasmic localization of p53. We found that K316P mutant mice develop several metabolic phenotypes, including increased body fat percentage, and increased liver lipid levels. In order to determine the mechanism through which K316P mutation increases liver lipid levels, we performed metabolomic analysis of mouse livers from WT and K316P mutant mice. Mouse livers were isolated from four wild type (WT) and four p53 K316P (M) mice for lipidomic analysis. Samples were isolated and flash frozen in liquid nitrogen. Lipids were then extracted from each liver sample and analyzed using mass spectrometry. |
| Institute | University of North Carolina |
| Last Name | Sanford |
| First Name | Jack |
| Address | 450 West Drive, Chapel Hill, NC, 27514 |
| jsan4d@email.unc.edu | |
| Phone | 3019284726 |
| Submit Date | 2022-12-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-12-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001543 |
| Project DOI: | doi: 10.21228/M87T4V |
| Project Title: | p53 K316P mouse liver lipidomics analysis |
| Project Summary: | Mouse livers were isolated from four wild type (WT) and four p53 K316P (M) mice for lipidomic analysis. Samples were isolated and flash frozen in liquid nitrogen. Lipids were then extracted from each liver sample and analyzed using mass spectrometry. |
| Institute: | University of North Carolina |
| Last Name: | Sanford |
| First Name: | Jack |
| Address: | 450 West Drive, Chapel Hill, NC, 27514 |
| Email: | jsan4d@email.unc.edu |
| Phone: | 3019284726 |
Subject:
| Subject ID: | SU002485 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | experimental factor(s) |
|---|---|---|
| SA239023 | WT-22R | p53 +/+ |
| SA239024 | WT-24R | p53 +/+ |
| SA239025 | WT-21RL | p53 +/+ |
| SA239026 | WT-8RL | p53 +/+ |
| SA239027 | m-6R | p53 K316P m/m |
| SA239028 | m-12L | p53 K316P m/m |
| SA239029 | m-41RL | p53 K316P m/m |
| SA239030 | m-6L | p53 K316P m/m |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO002478 |
| Collection Summary: | Mouse liver samples were collected from mice and immediately flash frozen in liquid nitrogen. Frozen tissue samples were crushed using a morter and pestle on dry ice to homogenize tissue prior to lipid extraction. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR002497 |
| Treatment Summary: | Male mice were C57BL/6J background, kept on a 12hr day/night cycle. Mice were 3-4 months old at the time of tissue isolation. Four littermate pairs were analyzed. |
Sample Preparation:
| Sampleprep ID: | SP002491 |
| Sampleprep Summary: | Mouse liver sections were weighed into Eppendorf tubes. The liver tissue was then mashed with a spatula prior to extraction. The samples were extracted using a liquid liquid partition with water (250 µL), methanol (300 µL), and MTBE (1 mL). Avanti’s deuterated lipid mix, Equisplash, was used as an internal standard. This was spiked into the methanol at 1.5 µg/mL and used for extraction. The extracts were centrifuged at 20,000 rcf for 10 min. The top layer was removed, dried down, and reconstituted in 1 mL of IPA for analysis. |
Combined analysis:
| Analysis ID | AN003903 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity H-Class |
| Column | Waters Acquity BEH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF-X Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH002889 |
| Chromatography Summary: | Analysis was performed using a Thermo Q Exactive Plus coupled to a Waters Acquity H-Class LC. A 100 mm x 2.1 mm, 1.7 µm Waters BEH C18 column was used for separations. The following mobile phases were used: A- 60/40 ACN/H20 B- 90/10 IPA/ACN; both mobile phases had 10 mM Ammonium Formate and 0.1% Formic Acid. A flow rate of 0.2 mL/min was used. Starting composition was 32% B, which increased to 40% B at 1 min (held until 1.5 min) then 45% B at 4 minutes. This was increased to 50% B at 5 min, 60% B at 8 min, 70% B at 11 min, and 80% B at 14 min (held until 16 min). At 16 min the composition switched back to starting conditions (32% B) and was held for 4 min to re-equilibrate the column. Samples were analyzed in positive/negative switching ionization mode with top 5 data dependent fragmentation. |
| Methods Filename: | Sanford_2022_Lipidomics_protocol.docx |
| Instrument Name: | Waters Acquity H-Class |
| Column Name: | Waters Acquity BEH C18 (100 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003642 |
| Analysis ID: | AN003903 |
| Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Analysis was performed using a Thermo Q Exactive Plus coupled to a Waters Acquity H-Class LC. A 100 mm x 2.1 mm, 2.1 µm Waters BEH C18 column was used for separations. The following mobile phases were used: A- 60/40 ACN/H20 B- 90/10 IPA/ACN; both mobile phases had 10 mM Ammonium Formate and 0.1% Formic Acid. A flow rate of 0.2 mL/min was used. Starting composition was 32% B, which increased to 40% B at 1 min (held until 1.5 min) then 45% B at 4 minutes. This was increased to 50% B at 5 min, 60% B at 8 min, 70% B at 11 min, and 80% B at 14 min (held until 16 min). At 16 min the composition switched back to starting conditions (32% B) and was held for 4 min to re-equilibrate the column. Samples were analyzed in positive/negative switching ionization mode with top 5 data dependent fragmentation. |
| Ion Mode: | UNSPECIFIED |
| Analysis Protocol File: | Sanford_2022_Lipidomics_protocol.docx |
