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MB Sample ID: SA177202
| Local Sample ID: | S_545 |
| Subject ID: | SU001991 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001991 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S_545 | SA177202 | FL021960 | Sample | Sample type |
Collection:
| Collection ID: | CO001984 |
| Collection Summary: | Infant stool samples were collected at home using provided diapers, sealed in a separate polyethylene bag and frozen in a home freezer or kept chilled until transport. Samples were transported in a cooler with ice packs and brought to the routine 6-week post-partum visit within 24 hours of collection. Stool samples remained frozen until processing where they were thawed at 4 °C. Using sterile applicators, 0.5–1 g of stool was aliquoted into trace element-free cryovial tubes and then frozen at −80 °C in a biorepository |
| Sample Type: | Feces |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002003 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP001997 |
| Sampleprep Summary: | De-identified stool aliquots were shipped on dry ice and immediately stored at -80 °C for metabolomics analysis. Samples were randomized into batches. For each batch, samples were thawed and ~150mg of stool was transferred to MagNA Lyser tubes after recording the weight, Samples were then homogenized with 50% acetonitrile in water by using the Omni Bead Disruptor (Omni International, GA, USA). Homogenized samples were centrifuged at 16000 rcf and the supernatant was separated into another tube. An aliquot (1000 uL, 100 mg equivalent of fecal mass) was transferred into Eppendorf tube and lyophilized overnight. The dried extract was reconstituted in 700 uL of NMR master mix (containing 0.2M phosphate, 0.5 mM DSS-d6, and 0.2% sodium azide), vortexed on a multitube vortexer at speed 5 for 2 min and centrifuged at 16000 rcf for 5 min. A 600 µl aliquot of the supernatant was transferred into a pre-labeled 5mm NMR tube for data acquisition on a 700 MHz spectrometer. Additionally, study pooled samples (created from randomly selected study samples) and batch pooled quality control (QC) samples were generated from supernatants of study samples and aliquots of supernatants were dried and reconstituted similar to study samples described above, and used for QC purposes. |
| Sampleprep Protocol Filename: | 1. Dartmouth-Fecal Metabolomics_NMR_Batch2 Procedures |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | 50% Acetonitrile in Water |
| Extract Storage: | -80℃ |
| Sample Resuspension: | In phosphate buffer containing D2O |
Analysis:
| MB Sample ID: | SA177202 |
| Analysis ID: | AN003111 |
| Laboratory Name: | Metabolomics and Exposome Lab at UNC Nutrition Research Institute |
| Analysis Type: | NMR |
| Software Version: | TopSpin 3.5 |
| Operator Name: | Wimal Pathmasiri |
| Detector Type: | NMR |
| Data Format: | fid, 1r |
| Results File: | 4a._Dartmouth-Fecal_Metabolomics_NMR_Normalized_Binned_Data.txt |
| Units: | ppm |
NMR:
| NMR ID: | NM000214 |
| Analysis ID: | AN003111 |
| Instrument Name: | Avance III 700 MHz NMR Spectrometer |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Field Frequency Lock: | 3015 Hz, D2O |
| Standard Concentration: | 0.5 mM |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | CP QCI/HPCN |
| NMR Solvent: | 90% H2O, 10% D2O |
| NMR Tube Size: | 5 mm |
| Shimming Method: | topshim |
| Pulse Sequence: | noesygppr1d |
| Water Suppression: | pre-saturation |
| Pulse Width: | 14.59 us |
| Power Level: | 12.3 Watts |
| Receiver Gain: | 36 |
| Offset Frequency: | 3290.61 Hz |
| Presaturation Power Level: | 0.0000964 Watts |
| Chemical Shift Ref Cpd: | DSS-d6 |
| Temperature: | 25 C |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 3.9 seconds |
| Relaxation Delay: | 2 seconds |
| Spectral Width: | 12 ppm |
| Num Data Points Acquired: | 65536 |
| Real Data Points: | 32768 |
| Line Broadening: | 0.5 Hz |
| Zero Filling: | Yes |
| Apodization: | Lorentzian |
| Baseline Correction Method: | Polynomial |
| Chemical Shift Ref Std: | DSS-d6 |
| Binned Increment: | 0.04ppm |
| Binned Data Excluded Range: | 4.79 - 4.85 ppm (Water region) |
