Return to study ST001366 main page
MB Sample ID: SA099369
Local Sample ID: | MALBG_2 |
Subject ID: | SU001440 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6J |
Age Or Age Range: | 7 weeks |
Gender: | Female |
Animal Animal Supplier: | Jackson Laboratories |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001440 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Genotype Strain: | C57BL/6J |
Age Or Age Range: | 7 weeks |
Gender: | Female |
Animal Animal Supplier: | Jackson Laboratories |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
MALBG_2 | SA099369 | FL014058 | MAL-BG | Treatment |
MALBG_2 | SA099369 | FL014058 | Malnourished | Diet |
MALBG_2 | SA099369 | FL014058 | Yes | Bacterial Exposure |
Collection:
Collection ID: | CO001435 |
Collection Summary: | Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics. |
Sample Type: | Hippocampus |
Treatment:
Treatment ID: | TR001455 |
Treatment Summary: | CON = control mice on healthy diet, MAL = mice placed on a protein/fat deficient diet (malnourished), MAL-BG = MAL mice plus iterative E.coli/Bacteroidales exposure |
Sample Preparation:
Sampleprep ID: | SP001448 |
Sampleprep Summary: | Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase (RP)-UPLC-FTMS. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively. |
Combined analysis:
Analysis ID | AN002273 | AN002274 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Waters BEH C8 (50 x 2.1mm,1.7um) | Waters BEH C8 (50 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo LTQ-Orbitrap Velos Pro | Thermo LTQ-Orbitrap Velos Pro |
Ion Mode | POSITIVE | NEGATIVE |
Units | abundance | abundance |
Chromatography:
Chromatography ID: | CH001672 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Waters BEH C8 (50 x 2.1mm,1.7um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002117 |
Analysis ID: | AN002273 |
Instrument Name: | Thermo LTQ-Orbitrap Velos Pro |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods). |
Ion Mode: | POSITIVE |
MS ID: | MS002118 |
Analysis ID: | AN002274 |
Instrument Name: | Thermo LTQ-Orbitrap Velos Pro |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | For relative quantitation, the MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods). |
Ion Mode: | NEGATIVE |