Summary of Study ST003528
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 PR002171. The data can be accessed directly via it's Project DOI: 10.21228/M80J8F 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 | ST003528 |
| Study Title | Lipidomics profiling of livers from Alb-Cre +/- SART-/- (KO) versus age matched wild type WT mouse littermates to characterize progression to hepatic steatosis and hepatocellular carcinoma |
| Study Summary | Mice bearing hepatocyte- specific deletion of the gene SART1 (Alb-Cre+/- SART-/-) develop hepatic steatosis at age 6 months and spontaneous liver tumors at age 18 months. To determine the changes in lipid composition of the SART1-deficient livers compared to age-matched wild- type livers, Liver lipidomics profiling of Male animals at different age groups were performed: Age 6 months: KO versus WT livers, Age 12 months: KO versus WT livers, Age 18 months: KO liver tumors versus WT livers. Flash-frozen livers from male Alb-Cre +/- SART1 +/+ (control) and Alb-Cre +/- SART-/- (KO) were subjected to lipidomics profiling. |
| Institute | University of Utah |
| Last Name | Koh |
| First Name | Mei Yee |
| Address | 30 S 2000E, SAlt Lake City, UT 84112 |
| mei.koh@utah.edu | |
| Phone | 801 581 4612 |
| Submit Date | 2024-09-27 |
| Num Groups | 3 |
| Total Subjects | 28 |
| Num Males | 28 |
| Publications | Hepatology 2024 (Akuna-Pilarte. et.al) DOI: 10.1097/HEP.0000000000001070 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002171 |
| Project DOI: | doi: 10.21228/M80J8F |
| Project Title: | Lipidomic Profiling of Livers from mice bearing hepatocyte-specific deletion of the SART1 (encoding the protein Hypoxia-associated Factor, HAF) compared to wild-type littermates to characterize progression to hepatic steatosis and hepatocellular carcinoma |
| Project Summary: | Mice bearing hepatocyte- specific deletion of the gene SART1 (Alb-Cre+/- SART-/-) develop hepatic steatosis at age 6 months and spontaneous liver tumors at age 18 months. To determine the changes in lipid composition of the SART1-deficient livers compared to age-matched wild- type livers, we performed lipidomics profiling of livers from mice of different ages. Flash-frozen livers from male Alb-Cre +/- SART1 +/+ (control) and Alb-Cre +/- SART-/- (KO) were subjected to lipidomics profiling. The following groups were used: Age 6 months: Control liver(5 mice), KO liver (5 mice) Age 12 months: Control liver (5 mice), KO liver (5 mice) Age 18 months: Control liver (5 mice), KO liver tumors (3 mice) |
| Institute: | University of Utah |
| Department: | Pharmacology and Toxicology |
| Laboratory: | Mei Koh |
| Last Name: | Koh |
| First Name: | Mei Yee |
| Address: | 30 S 2000E, Salt Lake City, UT 84112 |
| Email: | mei.koh@utah.edu |
| Phone: | 801 581 4612 |
| Funding Source: | NIH/NCI |
| Publications: | Hepatology 2024 (Akuna-Pilarte. et.al) DOI: 10.1097/HEP.0000000000001070 |
Subject:
| Subject ID: | SU003657 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Time |
|---|---|---|---|---|
| SA387269 | B-1 | liver | KO | 12 month |
| SA387270 | B-2 | liver | KO | 12 month |
| SA387271 | B-3 | liver | KO | 12 month |
| SA387272 | B-4 | liver | KO | 12 month |
| SA387273 | B-5 | liver | KO | 12 month |
| SA387274 | A-2 | liver | KO | 6 month |
| SA387275 | A-1 | liver | KO | 6 month |
| SA387276 | A-5 | liver | KO | 6 month |
| SA387277 | A-3 | liver | KO | 6 month |
| SA387278 | A-4 | liver | KO | 6 month |
| SA387279 | E-2 | liver | WT | 12 month |
| SA387280 | E-5 | liver | WT | 12 month |
| SA387281 | E-4 | liver | WT | 12 month |
| SA387282 | E-3 | liver | WT | 12 month |
| SA387283 | E-1 | liver | WT | 12 month |
| SA387284 | F-1 | liver | WT | 18 month |
| SA387285 | F-2 | liver | WT | 18 month |
| SA387286 | F-3 | liver | WT | 18 month |
| SA387287 | F-4 | liver | WT | 18 month |
| SA387288 | F-5 | liver | WT | 18 month |
| SA387289 | D-5 | liver | WT | 6 month |
| SA387290 | D-4 | liver | WT | 6 month |
| SA387291 | D-3 | liver | WT | 6 month |
| SA387292 | D-1 | liver | WT | 6 month |
| SA387293 | D-2 | liver | WT | 6 month |
| SA387266 | C-3T | liver tumor | KO | 18 month |
| SA387267 | C-5T | liver tumor | KO | 18 month |
| SA387268 | C-4T | liver tumor | KO | 18 month |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO003650 |
| Collection Summary: | Mice were euthanized and livers excised, sliced and snap frozen in liquid nitrogen. Frozen sections were further cut on dry ice into 25mg pieces and submitted for lipidomics profiling. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003666 |
| Treatment Summary: | Mice were maintained on regular chow and allowed to age naturally. Cohorts of control and KO animals were euthanized when they reached 6 months, 12 months and 18 months. |
Sample Preparation:
| Sampleprep ID: | SP003664 |
| Sampleprep Summary: | Total lipids were extracted from the tissue homogenate using the Matyash (MTBE) method. In a randomized sequence, ice cold 225 µL MeOH with internal standards (EQUISPLASH and palmitic acid-d31, Avanti Polar Lipids) and 188 µL PBS were added to each sample, which was then homogenized and transferred to microcentrifuge tubes containing 750 µL MTBE. After incubation on ice for 1 hour, the samples were centrifuged, and the organic layer was collected. The aqueous layer was re-extracted using a mix of MTBE, MeOH, and water, vortexed, incubated at room temperature, and centrifuged again. The upper phases were combined, evaporated, and the lipid extracts were reconstituted in IPA/ACN and transferred to LC-MS vials for analysis. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | -20℃ |
Combined analysis:
| Analysis ID | AN005795 | AN005796 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6545 QTOF | Agilent 6545 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | pmol per mg tissue | pmol per mg tissue |
Chromatography:
| Chromatography ID: | CH004400 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Started at 15% mobile phase B then increased to 30% B over 2.4 min, it then increased to 48% B from 2.4 – 3.0 min, then increased to 82% B from 3 – 13.2 min, then increased to 99% B from 13.2 – 13.8 min where it’s held until 16.7 min and then returned to the initial conditions and equilibriated for 5 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate and 0.1% formic acid |
| Solvent B: | 90% isopropanol/9% acetonitrile/1% water; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004401 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Started at 15% mobile phase B then increased to 30% B over 2.4 min, it then increased to 48% B from 2.4 – 3.0 min, then increased to 82% B from 3 – 13.2 min, then increased to 99% B from 13.2 – 13.8 min where it’s held until 16.7 min and then returned to the initial conditions and equilibriated for 5 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium carbonate |
| Solvent B: | 90% isopropanol/9% acetonitrile/1% water; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005515 |
| Analysis ID: | AN005795 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | For data processing, Agilent MassHunter (MH) Workstation and software packages MH Qualitative and MH Quantitative were used. The pooled QC (n=8) and process blank (n=4) were injected throughout the sample queue to ensure the reliability of acquired lipidomics data. For lipid annotation, accurate mass and MS/MS matching was used with the Agilent Lipid Annotator library and LipidMatch (14). Results from the positive and negative ionization modes from Lipid Annotator were merged based on the class of lipid identified. Data exported from MH Quantitative was evaluated using Excel where initial lipid targets are parsed based on the following criteria. Only lipids with relative standard deviations (RSD) less than 30% in QC samples were used for data analysis. Additionally, only lipids with background AUC counts in process blanks that are less than 30% of QC are used for data analysis. The parsed excel data tables are normalized based on the ratio to class-specific internal standards, then to tissue mass and sum prior to statistical analysis. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005516 |
| Analysis ID: | AN005796 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | For data processing, Agilent MassHunter (MH) Workstation and software packages MH Qualitative and MH Quantitative were used. The pooled QC (n=8) and process blank (n=4) were injected throughout the sample queue to ensure the reliability of acquired lipidomics data. For lipid annotation, accurate mass and MS/MS matching was used with the Agilent Lipid Annotator library and LipidMatch (14). Results from the positive and negative ionization modes from Lipid Annotator were merged based on the class of lipid identified. Data exported from MH Quantitative was evaluated using Excel where initial lipid targets are parsed based on the following criteria. Only lipids with relative standard deviations (RSD) less than 30% in QC samples were used for data analysis. Additionally, only lipids with background AUC counts in process blanks that are less than 30% of QC are used for data analysis. The parsed excel data tables are normalized based on the ratio to class-specific internal standards, then to tissue mass and sum prior to statistical analysis. |
| Ion Mode: | NEGATIVE |
