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MB Sample ID: SA002707
| Local Sample ID: | 1402110jcsa26_1 |
| Subject ID: | SU000073 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | female |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000073 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | female |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 1402110jcsa26_1 | SA002707 | FL000726 | LumA | Treatment |
| 1402110jcsa26_1 | SA002707 | FL000726 | no | Collection Time (h) |
Collection:
| Collection ID: | CO000056 |
| Collection Summary: | Cancer-adjacent, normal breast tissue was collected |
| Collection Protocol ID: | UNC-CH IRB #09-1436 |
| Collection Protocol Filename: | Normal_Breast_Study |
| Collection Protocol Comments: | Breast tissue samples were collected from patients in the UNC hospital system under the Normal Breast Study (IRB #09-1436). Normal breast tissue from patients with reduction mammoplasty, DCIS and invasive breast cancer were analyzed in this study. Tissue samples 2-4 cm away from the tumor were collected and stored at -80°C after surgery. Samples were cut on dry ice to yield a metabolomics sample comprising 50-120 mg tissue. The tissue was placed in a tissue homogenization tube with ceramic beads and stored at -80°C. The samples were delivered to the RTI RCMRC and stored at -80°C. |
| Sample Type: | tissue |
| Collection Method: | tissue collected during surgery |
| Collection Location: | breast microenvironment |
| Collection Frequency: | one time collection |
| Volumeoramount Collected: | 50 - 120mg |
| Storage Conditions: | -80 C |
| Tissue Cell Identification: | breast |
| Tissue Cell Quantity Taken: | 50mg |
Treatment:
| Treatment ID: | TR000074 |
| Treatment Summary: | Stages of breast cancer progression and different subtypes compared to a non-malignant control |
| Treatment Protocol Comments: | DCIS, Luminal A, Luminal B, HER2, Basal, Reduction, Total Pool1 (equal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples),Total Pool2 (unequal mix of DCIS, HER2, LumA, LumB, Reduction, and Basal pool samples) |
Sample Preparation:
| Sampleprep ID: | SP000069 |
| Sampleprep Summary: | Breast tissue samples were homogenized in 3:3:2 (acetonitrile:isopropanol:water) at a concentration of 100 mg/mL. Samples dried and extracted into 50% acetonitrile. Sample dried and aliquot taken for NMR. Sample returned and extract processed for GC/MS analysis. Samples were derivatized using 2 step derivatization method (methoximation with methoxy amine followed by TMS derivatization with MSTFA). |
| Sampleprep Protocol Filename: | RTI_MT_Breast_Tissue_Procedures_GC-TOF-MS.docx |
| Processing Method: | Homogenization and Solvent Removal with SpeedVac |
| Processing Storage Conditions: | 4°C |
| Extraction Method: | 3:3:2 (acetonitrile:isopropanol:water) and then 50% Acetonitrile |
| Extract Concentration Dilution: | dried on SpeedVac |
| Extract Storage: | -80°C |
| Sample Resuspension: | resuspended in D2O + Chenomix ISTD solution |
| Sample Derivatization: | Methoximation with methoxy amine at 40 mg/ml in pyridine followed by TMS derivatization with MSTFA |
| Sample Spiking: | FAMES (C8-C30) added to MSTFA as retention time markers |
Combined analysis:
| Analysis ID | AN000092 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus 4D GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC x GC-TOF |
| MS instrument name | Leco Pegasus 4D GCxGC TOF |
| Ion Mode | POSITIVE |
| Units | Peak height |
Chromatography:
| Chromatography ID: | CH000060 |
| Chromatography Summary: | GC/MS analysis is based on Oliver Fiehn methods |
| Instrument Name: | Leco Pegasus 4D GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Pressure: | 10.4 psi |
| Column Temperature: | 50C(0.5 min)-330C(@20C/min)-330C(5 min) |
| Flow Gradient: | constant flow |
| Flow Rate: | 1.0 mL/min |
| Injection Temperature: | 250C |
| Retention Index: | FAMEs markers (C8-C30) |
| Retention Time: | FAMEs markers (C8-C30) |
| Analytical Time: | 20 minutes |
| Oven Temperature: | 50C(0.5 min)-330C(@20C/min)-330C(5 min) |
| Transferline Temperature: | 280C |
| Sample Syringe Size: | 10 L |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000069 |
| Analysis ID: | AN000092 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 280C (transfer line) |
| Helium Flow: | 1.0 ml/min |
| Ion Source Temperature: | 250C |
| Ionization Energy: | 70 eV |
| Source Temperature: | 250C |
| Dataformat: | netcdf |
| Resolution Setting: | 1200 |
| Scan Range Moverz: | 50-800 |
| Scanning: | 20 spectra/sec |
