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MB Sample ID: SA001195
| Local Sample ID: | 3130-RV |
| Subject ID: | SU000037 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 56-78 |
| Weight Or Weight Range: | Obese or Overweight |
| Gender: | Male, Female |
| Human Race: | Caucasian, African American |
| Human Trial Type: | Intervention |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000037 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 56-78 |
| Weight Or Weight Range: | Obese or Overweight |
| Gender: | Male, Female |
| Human Race: | Caucasian, African American |
| Human Trial Type: | Intervention |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 3130-RV | SA001195 | FL000424 | RV | Time Point |
| 3130-RV | SA001195 | FL000424 | N | Progressor |
| 3130-RV | SA001195 | FL000424 | Diet Only | Intervention |
| 3130-RV | SA001195 | FL000424 | W | Race |
| 3130-RV | SA001195 | FL000424 | F | gender |
Collection:
| Collection ID: | CO000020 |
| Collection Summary: | Urine samples (early morning [second morning void) after a 10-hour fast]) collected from 44 overweight or obese participants in the IDEA trial at baseline and at 18 months of follow-up were selected from two subgroups (n=22 each): a group that exhibited radiographic progression and an age, race, sex, and BMI matched group who did not progress. Progression was defined radiographically by a ≥ 0.7mm decrease in medial JSW from baseline to 18 months while non-progression was defined as a decrease in medial JSW of ≤0.35mm . All subjects experienced knee pain and had radiographic evidence of tibiofemoral OA. For those people who were assigned an intervention that included exercise, the 18-month samples were collected at least 24 hours after the last acute bout of exercise training. In addition sampling was postponed (1-2 weeks after recovery from symptoms) in the event of an acute respiratory, urinary tract, or other infection. Urine was aliquoted and stored in cryovials at -80°C. |
| Sample Type: | Urine |
| Collection Frequency: | Baseline and after 18 month (Follow up) |
| Volumeoramount Collected: | 1.8 mL of urine |
| Storage Conditions: | 80C. |
Treatment:
| Treatment ID: | TR000038 |
Sample Preparation:
| Sampleprep ID: | SP000033 |
| Sampleprep Summary: | Chenomx Internal Standard solution (70 ul) and 230 ul D20 was added to each of the 88 urine sample (400 ul), vortexed for 30s, and centrifuged at 12000 rcf for 5min. Chenomx ISTD (Chenomx, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) in D2O. 600 µl aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany). Phenotypic pooled urine samples were made by combining 200 µl aliquots from each of the study samples belonging to the same phenotype (Progressors-Baseline, Progressors-follow up, Non-progressors-baseline, and Non-progressors-follow up). In addition, a combined phenotypic pooled sample was also prepared by using 500 µl aliquot from each of the phenotypic pooled sample. Pooled NMR samples were prepared as described above and used as quality check (QC) samples. |
| Sampleprep Protocol ID: | RTI NMR SERUM CHENOMX method |
| Sampleprep Protocol Filename: | RTI_WOA_IDEA_Metabolomics_Procedure_Feb28_2014.docx |
| Processing Method: | Dilution using a mixture of D2O and Chenomx ISTD |
| Processing Storage Conditions: | On ice |
| Extraction Method: | None |
Analysis:
| MB Sample ID: | SA001195 |
| Analysis ID: | AN000039 |
| Laboratory Name: | RTI/DHMRI |
| Analysis Type: | NMR |
| Acquisition Date: | 2013-07-17 |
| Software Version: | Topspin/ 3.0 |
| Operator Name: | Wimal Pathmasiri, Kevin Knagge |
| Randomization Order: | Yes |
| Data Format: | fid, 1r |
| Chromatography ID: | CH000021 |
| Num Factors: | 34 |
| Num Metabolites: | 24 |
NMR:
| NMR ID: | NM000005 |
| Analysis ID: | AN000039 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5 mM |
| Spectrometer Frequency: | 950 MHz |
| NMR Probe: | cryo, inverse ATMA |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm x 7 in |
| Shimming Method: | topshim |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presat |
| Pulse Width: | 12.15 us |
| Power Level: | 12.589w |
| Receiver Gain: | 4 |
| Offset Frequency: | 4469.3 Hz |
| Chemical Shift Ref Cpd: | DSS |
| Temperature: | 298 K |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 0.865 sec |
| Relaxation Delay: | 2 sec |
| Spectral Width: | 18939.40 Hz |
| Num Data Points Acquired: | 32K |
| Real Data Points: | 64K |
| Line Broadening: | 0.5 |
| Zero Filling: | yes |
| Apodization: | lorentzian |
| Baseline Correction Method: | Polynomial |
| Chemical Shift Ref Std: | DSS |
