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MB Sample ID: SA201156
| Local Sample ID: | pooled_pd1074_91 |
| Subject ID: | SU002180 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002180 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| pooled_pd1074_91 | SA201156 | FL024453 | 2 | set |
| pooled_pd1074_91 | SA201156 | FL024453 | 4 | batch |
| pooled_pd1074_91 | SA201156 | FL024453 | pooled_pd1074 | genotype |
Collection:
| Collection ID: | CO002173 |
| Collection Summary: | Escherichia coli (E. coli) IBAT (iterative batch average method) reference material and food source used throughout this experiment. Briefly, for each biological sample, a large-scale culture plate (LSCP) was used to generate a large mixed-stage population of worms (four to seven LSCP replicates per test strain). For each LSCP, worms were collected, population size estimated, and subsequently divided into at least 12 identical aliquots of 200,000 worms in ddH2O and flash-frozen in liquid nitrogen and stored at -80°C. As a quality control sample, C. elegans IBAT reference material was generated and saved in 200,000 worm aliquots. |
| Sample Type: | Worms |
| Volumeoramount Collected: | 200,000 worms |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002192 |
| Treatment Summary: | No treatments. |
Sample Preparation:
| Sampleprep ID: | SP002186 |
| Sampleprep Summary: | Frozen lyophilized C. elegans aliquots were retrieved from -80°C. 200 μL of 1 mm zirconia beads were added to each sample and homogenized at 420 rcf for 90 seconds in a FastPrep-96 homogenizer and subsequently placed on dry ice for 90 seconds to avoid overheating, this step was repeated twice for a total of three rounds. Using the homogenized samples, 1 mL of 100% IPA chilled to -20°C was added to the lyophilized/homogenized sample powder and Zirconia beads in two increments of 500 μL. After each addition of 500 μL, samples were vortexed for 30 seconds – 1 minute and left at RT for 15 - 20 minutes. After RT incubation, samples were stored overnight (~12 hours) at -20°C. Samples were centrifuged for 30 minutes at 4°C (20,800 rcf). The supernatant was transferred to a new tube to use for analysis of non-polar molecules. 1 mL of pre-chilled 80:20 MeOH:H2O (4°C) was added to the remaining worm pellet to analyze polar molecules. The polar fraction shook at 4°C for 30 minutes. Samples were centrifuged at 20,800 rcf for 30 minutes at 4°C. The supernatant was transferred to a new tube to use for analysis of non-polar molecules. Both polar and non-polar samples were placed in a Labconco Centrivap at RT and monitored until completely dry. Once dry, polar and non-polar samples were reconstituted in D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) and CDCl3 (99.96%, Cambridge Isotope Laboratories, Inc.) respectively. Samples were vortexed until fully soluble, and 45 μL of each sample were transferred into 1.7 mm NMR tubes (Bruker SampleJet) for acquisition. |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Sequential extraction of (1) IPA for non-polar molecule followed by (2) 80/20 MeOH/H2O for polar |
| Extract Storage: | -80℃ |
| Sample Resuspension: | CDCl3 for non-polar; D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) for polar |
Analysis:
| MB Sample ID: | SA201156 |
| Analysis ID: | AN003424 |
| Laboratory Name: | Edison Lab – Complex Carbohydrate Research Center |
| Analysis Type: | NMR |
| Acquisition Date: | 2020-03-30 |
| Operator Name: | Amanda O. Shaver |
| Detector Type: | Bruker Neo 1.7 mm TCI Cryo Probe |
| Data Format: | ft |
| Results File: | ST002096_AN003424_Results.txt |
| Units: | Ranked Intensity |
NMR:
| NMR ID: | NM000233 |
| Analysis ID: | AN003424 |
| Instrument Name: | Bruker Neo 800 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 |
| NMR Probe: | 1.7 mm TCI cryoprobe |
| NMR Solvent: | CDCl3 |
| NMR Tube Size: | 1.7 mm |
| Shimming Method: | Automatic (“Topshim”) |
| Pulse Sequence: | zg |
| Water Suppression: | 3758.64 @ 4.7 ppm |
| Receiver Gain: | 65.1 |
| Temperature: | 6 |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 1.31 sec |
| Spectral Width: | 20.2 |
| Num Data Points Acquired: | 65,536 |
| Line Broadening: | 1.5 |
| Apodization: | exponential |
| Baseline Correction Method: | Polynomial Automatic fit |
| Chemical Shift Ref Std: | 7.24 |
