Return to study ST000391 main page
MB Sample ID: SA018464
| Local Sample ID: | 120412_lung_tissue_Sample56 |
| Subject ID: | SU000412 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 55-91 |
| Gender: | M/F |
| Human Race: | Caucasian, Asian |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000412 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 55-91 |
| Gender: | M/F |
| Human Race: | Caucasian, Asian |
| Human Smoking Status: | Current vs. former |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 120412_lung_tissue_Sample56 | SA018464 | FL005196 | M | Sex |
| 120412_lung_tissue_Sample56 | SA018464 | FL005196 | Current Smoker | Smoking Status |
| 120412_lung_tissue_Sample56 | SA018464 | FL005196 | adenocarcinoma w/ BAC | Diagnosis |
| 120412_lung_tissue_Sample56 | SA018464 | FL005196 | Yes | Tumor Present |
Collection:
| Collection ID: | CO000406 |
| Collection Summary: | Deidentified malignant and adjacent nonmalignant lung tissue was obtained from the New York University biorepository. Residual tumor and adjacent nonmalignant tissue was harvested from the resected lung after routine pathologic protocols were completed, following an approved Institutional Review Board (IRB) protocol with patient consent. Two to three tissue pieces were aliquoted into 1.5 mL Nunc vials, and then immediately placed in liquid nitrogen. After transport in liquid nitrogen, each vial was barcoded and stored at 80 C until analyzed. |
| Collection Protocol Filename: | Cancer_Prev_Res-2015-Wikoff-410-8.pdf |
| Sample Type: | Tissue |
Treatment:
| Treatment ID: | TR000426 |
| Treatment Summary: | All specimens were clinically annotated for age, gender, race, histology, smoking status, pack-years, and stage of disease. For this clinical study, samples were selected that came from patients who met the following criteria: (i) current or former smokers, (ii) adenocarcinoma histology, (iii) pathologic stage IA or IB, and (iv) had understood and signed the IRB consent form. |
| Treatment Protocol Filename: | Cancer_Prev_Res-2015-Wikoff-410-8.pdf |
Sample Preparation:
| Sampleprep ID: | SP000419 |
| 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 | AN000627 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 6530 |
| Column | Waters Acquity BEH HILIC (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6530A QTOF |
| Ion Mode | POSITIVE |
| Units | counts |
Chromatography:
| Chromatography ID: | CH000452 |
| Methods Filename: | LungNodule_HILIC_Pos_101_AcqMethodReport.pdf |
| Instrument Name: | Agilent 6530 |
| Column Name: | Waters Acquity BEH HILIC (150 x 2.1mm,1.7um) |
| Column Pressure: | 1200 bar |
| Column Temperature: | 45 C |
| Flow Gradient: | 100%B to 45% B |
| Flow Rate: | 0.4 mL/min |
| Sample Injection: | 5uL |
| Solvent A: | 100% water; 4 mM acetic acid; 6 mM ammonium acetate |
| Solvent B: | 90% acetonitrile/10% water; 4 mM acetic acid; 6 mM ammonium acetate |
| Analytical Time: | 20 min |
| Randomization Order: | Excel generated |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000560 |
| Analysis ID: | AN000627 |
| Instrument Name: | Agilent 6530A QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3000 V |
| Dry Gas Flow: | 8 L/min |
| Dry Gas Temp: | 350 C |
| Fragment Voltage: | 125 V |
| Ionization: | Pos |
| Mass Accuracy: | Nominal |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 V |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 57-1400 Da |
| Skimmer Voltage: | 65 V |
