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MB Sample ID: SA018502
| Local Sample ID: | 140518bjlsa23_2 |
| Subject ID: | SU000413 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 50-92 |
| Gender: | M/F |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000413 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 50-92 |
| Gender: | M/F |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 140518bjlsa23_2 | SA018502 | FL005070 | Plasma | Organ |
| 140518bjlsa23_2 | SA018502 | FL005070 | cancer | Disease State |
| 140518bjlsa23_2 | SA018502 | FL005070 | F | Gender |
| 140518bjlsa23_2 | SA018502 | FL005070 | Former | Smoking Status |
Collection:
| Collection ID: | CO000407 |
| Collection Summary: | Pre-existing patient blood samples were acquired from the biorepositories of two institutions (FHCRC and UCDMC), all collected and stored at −80 °C before use in these metabolomics studies. All patient samples for Study 1 (cases) were collected during a clinic visit prior to surgery for resectable early stage lung cancer and the controls were collected from clinic subjects without lung cancer. For Study 2, samples were acquired from University of California at Davis Medical Center (UCDMC) and included a variety of lung cancers. For Study 1, 20 control subjects were compared to 18 cases. Data from two samples were not included in the analysis due to low analytical results for these samples. |
| Collection Protocol Filename: | Metabolomic_Changes_in_Blood_Samples_of_Lung_Cancer_Patients.pdf |
| Sample Type: | Blood |
| Blood Serum Or Plasma: | Both |
Treatment:
| Treatment ID: | TR000427 |
| Treatment Summary: | Blood samples (plasma) in Study 1 (FHCRC study) were taken from newly diagnosed lung cancer patients with NSCLC adenocarcinoma (mostly late stage) and were frequency matched with for age, gender and for general smoking history (current and former smokers). Controls for this study were blood samples collected from individuals who were cancer free and with no history of cancer and who were current or former smokers. The second set of blood samples (Study 2) came from patients diagnosed with lung cancers (different types) (11 cases) that were frequency matched (age and gender) with samples from individuals without cancer and with no history of cancer (11 controls). These samples were obtained from the UC Davis Cancer Center Biorepository (CCB) and the UC Davis Clinical laboratory at the UC Davis Medical Center (UCDMC). Smoking history and treatment status were known for most of the cases in Study 2, but not known for some of the control group. Fasting status of patients and controls were unknown. All blood samples (plasma and serum) were prepared using standard clinical SOPs specified at each institution and stored at -80 °C until use. |
| Treatment Protocol Filename: | Metabolomic_Changes_in_Blood_Samples_of_Lung_Cancer_Patients.pdf |
Sample Preparation:
| Sampleprep ID: | SP000420 |
| Sampleprep Summary: | 1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30μl of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450μL portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450μL aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 μL 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_blood-GCTOF-11082012.pdf |
Combined analysis:
| Analysis ID | AN000628 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Corporation Rtx-5Sil MS |
| MS Type | EI |
| MS instrument type | GC Ion Trap |
| MS instrument name | Varian 210-MS GC Ion Trap |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000453 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf |
| Instrument Name: | Agilent 6890N |
| 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: | MS000561 |
| Analysis ID: | AN000628 |
| Instrument Name: | Varian 210-MS GC Ion Trap |
| Instrument Type: | GC Ion Trap |
| 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 |
