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MB Sample ID: SA020204
| Local Sample ID: | 140404ajlsa28_1 |
| Subject ID: | SU000433 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000433 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 140404ajlsa28_1 | SA020204 | FL006490 | fresh liver | Treatment |
| 140404ajlsa28_1 | SA020204 | FL006490 | 2 Hr | Collection Time |
Collection:
| Collection ID: | CO000427 |
| Collection Summary: | Liver biopsies were frozen in liquid nitrogen and then stored at -80. They were then pulverized and the crushed tissue from one biopsy was divided into three 0.6mL tubes, containing ±25-70mg. These are triplicates from each biopsy. Tissue was kept at cryo temperatures throughout. |
| Collection Protocol Filename: | StudyDesign_BoteBruinsma_02.11.14.pdf |
| Sample Type: | Tissue |
Treatment:
| Treatment ID: | TR000447 |
| Treatment Summary: | 9 livers were run for metabolites at 4 timepoints (0,1,2,3), in triplicate. Warm ischemic livers (27, 8, 34) and non-warm ischemic livers (25, 28, 35) and fresh liver samples (R). Liver 30 was a steatotic liver, for which there were 4 timepoints. |
| Treatment Protocol Filename: | StudyDesign_BoteBruinsma_02.11.14.pdf |
Sample Preparation:
| Sampleprep ID: | SP000440 |
| Sampleprep Summary: | 1. Weigh 4 mg tissue sample ( muscle 20 mg) in to a 2.0 ml eppendorf tube. Add 1.0 mL extraction solvent to the tissue sample and using GenoGrinder homogenize samples for 45 seconds ensuring that sample resembles a powder. 2. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 3. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 4. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) (only for liver and brain samples). 5. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 6. Remove supernatant to a new Eppendorff tube. 7. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 8. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Liver_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000652 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus III GC |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000470 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Leco Pegasus III GC |
| Column Name: | Restek Corporation Rtx-5Sil MS |
| Column Pressure: | 7.7 PSI |
| Column Temperature: | 50-330C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50 C ramped to 250 C by 12 C/s |
| Sample Injection: | 0.5 uL |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000578 |
| Analysis ID: | AN000652 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250 C |
| Ionization Energy: | 70 eV |
| Mass Accuracy: | Nominal |
| Source Temperature: | 250 C |
| Scan Range Moverz: | 85-500 Da |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 85-500 Da |
| Skimmer Voltage: | 1850 V |
