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MB Sample ID: SA001420
| Local Sample ID: | D0945 |
| Subject ID: | SU000039 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | Average age 68.1(9.12) |
| Weight Or Weight Range: | Average BMI of 31.4(7.01) |
| Gender: | Male, Female |
| Species Group: | Human |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000039 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | Average age 68.1(9.12) |
| Weight Or Weight Range: | Average BMI of 31.4(7.01) |
| Gender: | Male, Female |
| Species Group: | Human |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| D0945 | SA001420 | FL000516 | Control | Disease Status |
Collection:
| Collection ID: | CO000022 |
| Collection Summary: | Urine samples (second morning void) collected from 36 overweight or obese participants in the JoCo at T1 or T1* were selected from two subgroups (a group that developed radiographic osteoarthritis (n=16) and an age, race, sex, and BMI matched group that did not develop osteoarthritis (n=20). Radiographic knee OA was defined as Kellgren-Lawrence grade 2-4 at T2 in a person with Kellgren-Lawrence grade 0 or 1 at T1 or T1*. |
| Sample Type: | Urine |
| Storage Conditions: | -80C |
Treatment:
| Treatment ID: | TR000040 |
Sample Preparation:
| Sampleprep ID: | SP000035 |
| Sampleprep Summary: | Chenomx Internal Standard solution (70 ul) and 230 ul D20 was added to each of the 36 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 l aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany). Phenotypic pooled urine samples were made by combining 150 l aliquots from each of the study samples belonging to the same phenotype (cases and control). In addition, a combined phenotypic pooled sample was prepared by using 1000 l 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 Filename: | Johnston_County_Procedure_March_4_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: | SA001420 |
| Analysis ID: | AN000041 |
| Laboratory Name: | RTI, DHMRI |
| Analysis Type: | NMR |
| Acquisition Date: | 41527 |
| Software Version: | TopSpin 3.0 |
| Operator Name: | Wimal Pathmasiri, Kevin Knagge |
| Randomization Order: | Yes |
| Detector Type: | NMR |
| Data Format: | Bruker |
| Chromatography ID: | CH000023 |
| Num Factors: | 2 |
NMR:
| NMR ID: | NM000007 |
| Analysis ID: | AN000041 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5mm |
| Spectrometer Frequency: | 950 MHz |
| NMR Probe: | 5mm, Inverse ATMA |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm, 7 inch |
| Shimming Method: | Topshim |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presat |
| Pulse Width: | 13.07 us |
| Power Level: | 12.589w |
| Receiver Gain: | 4 |
| Offset Frequency: | 4468.31 |
| Chemical Shift Ref Cpd: | DSS |
| Temperature: | 298 K |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 1.7301503 s |
| Relaxation Delay: | 2 s |
| Spectral Width: | 18939.395 Hz, 19.93 ppm |
| Num Data Points Acquired: | 65536 |
| Real Data Points: | 65536 |
| Line Broadening: | 0.5 |
| Zero Filling: | Yes |
| Apodization: | Lorentzian |
| Baseline Correction Method: | Polynomial |
| Chemical Shift Ref Std: | DSS |
