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MB Sample ID: SA001769
| Local Sample ID: | Test_3P |
| Subject ID: | SU000057 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
| Genotype Strain: | N2 |
| Age Or Age Range: | Young Adult |
| Gender: | Hermaphrodite |
| Species Group: | Invertebrate |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000057 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
| Genotype Strain: | N2 |
| Age Or Age Range: | Young Adult |
| Gender: | Hermaphrodite |
| Species Group: | Invertebrate |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Test_3P | SA001769 | FL000591 | heat shock | Heat shock |
| Test_3P | SA001769 | FL000591 | endometabolome | Metabolome |
Collection:
| Collection ID: | CO000040 |
| Collection Summary: | - |
| Sample Type: | whole young adult C. elegans Heat shock | supernatant Heat shock | whole young adult C. elegans Control | supernatant Control |
| Collection Method: | centrifugation | Filtration (0.2 micron) | centrifugation | Filtration (0.2 micron) |
| Volumeoramount Collected: | 225,000 worms | 10 mL worm water | 250,000 worms | 10 mL worm water |
Treatment:
| Treatment ID: | TR000058 |
| Treatment Summary: | Heat Shock: Two successive synchronous generations of wild-type C. elegans (N2) were grown in S-complete buffer at 22C containing 5% 13C-labeled E. coli. Upon reaching the young adult stage, the population was washed from E. coli using standard procedures and was divided into four replicates. Each replicate was treated with a 30 min heat shock at 33 °C followed by incubation at 22C for 1.5 hours. Control: Two successive synchronous generations of wild-type C. elegans (N2) were grown in S-complete buffer at 22C containing 95% 13C-labeled E. coli. Upon reaching the young adult stage, the population was washed from E. coli using standard procedures. |
| Treatment: | Abiotic |
| Treatment Dose: | 30C | 22C |
| Treatment Doseduration: | 30C for 30 minutes; 1.5 hours at 22 C before harvest | 22C for 30 minutes; 1.5 hours at 22 C before harvest |
| Animal Acclimation Duration: | - |
Sample Preparation:
| Sampleprep ID: | SP000053 |
| Sampleprep Summary: | Supernatant (endometabolome) was separated from worm pellets (exometabolome) by centrifugation. The supernatant was filtered, lyophilized, and resuspended in 100 μL of LC-MS grade H2O. Worm pellet (endometabolome)was separated from supernatant (exometabolome) by centrifugation. The worm pellets were homogenized using a Biospec Mini-Beadbeater-8 in 80% methanol, dried under nitrogen and resuspended in 100 μL of LC-MS grade H2O. |
| Processing Method: | filtration with 0.2 micron nitrocellulose, frozen at -80C, lyophilized and resuspended in 100 μL of LC-MS grade H2O. homogenization with Biospec Mini-Beadbeater-8 in 80% methanol, dried under nitrogen and resuspended in 100 μL of LC-MS grade H2O. |
Combined analysis:
| Analysis ID | AN000060 | AN000061 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Accela 1250 | Thermo Accela 1250 |
| Column | Thermo Scientific Gold aQ | Thermo Scientific Gold aQ |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH000041 |
| Chromatography Summary: | Three microliters of each sample were injected onto a Thermo Scientific Gold aQ (150 × 2.1 mm, 1.9 μm) column using a column temperature of 40 °C and a flow rate of 600 μL/min with a gradient of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) from 100% solvent A for 1 min followed by a linear gradient to 20% B in 6 min, a linear gradient to 60% B in 2 min, a linear gradient to 95% B in 4 min, held for 2 min, and a 3.5 min return to the starting composition. The inlet to the Orbitrap was held at a temperature of 320 °C, and the S-lens RF Level was set to 35%. The FR resolution was set to 70 000 at m/z 200. The accuracy achieved was routinely less than 1.5 ppm, externally calibrated. |
| Instrument Name: | Thermo Accela 1250 |
| Column Name: | Thermo Scientific Gold aQ |
| Column Temperature: | 40 °C |
| Flow Gradient: | A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile) from 100% solvent A for 1 min followed by a linear gradient to 20% B in 6 min, a linear gradient to 60% B in 2 min, a linear gradient to 95% B in 4 min, held for 2 min, and a 3.5 min return to the starting composition |
| Sample Injection: | 3 ?L |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 18.5 min |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000041 |
| Analysis ID: | AN000060 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed using a mass range of m/z 70-800 in positive and negative ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass spectrometer equipped with an Open Accela autosampler and an Accela 1250 pump (San Jose, CA). The Q-Exactive was equipped with a heated electrospray ionization (HESI) source, which operated at a spray temperature of 500 °C, a spray voltage of 3 kV, and sheath and auxiliary gas flow rates of 60 and 10 arbitrary units, respectively. Features were extracted from the ms data using proprietary MATLAB IROA scripts. Ratios for each feature (heatshock/control) were calculated for each replicate. Ratios were normalized by setting the median log-fold change for each sample to zero |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 500 °C |
| Ion Spray Voltage: | 3 kV |
| Mass Accuracy: | 1.5 ppm |
| Scan Range Moverz: | 70-1000 |
| MS ID: | MS000042 |
| Analysis ID: | AN000061 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed using a mass range of m/z 70-800 in positive and negative ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive Orbitrap mass spectrometer equipped with an Open Accela autosampler and an Accela 1250 pump (San Jose, CA). The Q-Exactive was equipped with a heated electrospray ionization (HESI) source, which operated at a spray temperature of 500 °C, a spray voltage of 3 kV, and sheath and auxiliary gas flow rates of 60 and 10 arbitrary units, respectively. Features were extracted from the ms data using proprietary MATLAB IROA scripts. Ratios for each feature (heatshock/control) were calculated for each replicate. Ratios were normalized by setting the median log-fold change for each sample to zero |
| Ion Mode: | NEGATIVE |
| Ion Source Temperature: | 500 °C |
| Ion Spray Voltage: | 3 kV |
| Mass Accuracy: | 1.5 ppm |
| Scan Range Moverz: | 70-1000 |
