Summary of Study ST000102
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000094. The data can be accessed directly via it's Project DOI: 10.21228/M8X309 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000102 |
| Study Title | Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster |
| Study Type | Time course during cold exposure for four genetic lines of flies |
| Study Summary | Metabolites of cold hardy versus cold susceptible flies were compared using N less than R-based metabolomics. We used 8 replicates per line (2 hardy lines, two susceptible lines), and sampled each line at three time points (before, during and after cold), giving rise to 96 samples total. |
| Institute | University of Florida |
| Department | Entomology and Nematology |
| Last Name | Williams |
| First Name | Caroline |
| cmw@berkeley.edu | |
| Submit Date | 2014-09-26 |
| Num Groups | 4 |
| Total Subjects | 96 |
| Raw Data Available | Yes |
| Uploaded File Size | 151 M |
| Analysis Type Detail | NMR |
| Release Date | 2015-02-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000094 |
| Project DOI: | doi: 10.21228/M8X309 |
| Project Title: | Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster |
| Project Type: | Genetic study |
| Project Summary: | Flies that had been selected for fast and slow recovery from a cold-coma (2 replicates of each type) were sampled before, during (at the end of a 3h cold exposure at 0 degC), and after 5 min recovery from cold exposure. We tested the hypothesis that cold adaptation remodelled metabolic networks to make them more robust to the effects of cold. |
| Institute: | University of Florida |
| Department: | Entomology and Nematology |
| Laboratory: | Daniel A. Hahn |
| Last Name: | Hahn |
| First Name: | Daniel |
| Email: | dahahn@ufl.edu |
| Funding Source: | NSF IOS-1051890 |
Subject:
| Subject ID: | SU000121 |
| Subject Type: | Insect |
| Subject Species: | Drosophila melanogaster |
| Taxonomy ID: | 7227 |
| Genotype Strain: | Originating from same base population as Drosophila melanogaster genetic reference panel, selected for fast (hardy) and slow (susceptible) recovery from chill coma. |
| Age Or Age Range: | 5-7 day-old adults (mated) |
| Weight Or Weight Range: | 0.17-0.77mg |
| Height Or Height Range: | NA |
| Gender: | Female |
| Animal Housing: | 25 degC |
| Animal Light Cycle: | 12L:12D |
| Animal Feed: | Standard cornmeal molasses medium |
| Animal Water: | in diet only |
| Species Group: | Insect |
Factors:
Subject type: Insect; Subject species: Drosophila melanogaster (Factor headings shown in green)
| mb_sample_id | local_sample_id | time |
|---|---|---|
| SA005573 | 238 | after | hardiness:hardy | population replicate:1 |
| SA005574 | 231 | after | hardiness:hardy | population replicate:1 |
| SA005575 | 232 | after | hardiness:hardy | population replicate:1 |
| SA005576 | 237 | after | hardiness:hardy | population replicate:1 |
| SA005577 | 236 | after | hardiness:hardy | population replicate:1 |
| SA005578 | 234 | after | hardiness:hardy | population replicate:1 |
| SA005579 | 235 | after | hardiness:hardy | population replicate:1 |
| SA005580 | 233 | after | hardiness:hardy | population replicate:1 |
| SA005581 | 531 | after | hardiness:hardy | population replicate:2 |
| SA005582 | 536 | after | hardiness:hardy | population replicate:2 |
| SA005583 | 538 | after | hardiness:hardy | population replicate:2 |
| SA005584 | 533 | after | hardiness:hardy | population replicate:2 |
| SA005585 | 537 | after | hardiness:hardy | population replicate:2 |
| SA005586 | 535 | after | hardiness:hardy | population replicate:2 |
| SA005587 | 534 | after | hardiness:hardy | population replicate:2 |
| SA005588 | 532 | after | hardiness:hardy | population replicate:2 |
| SA005589 | 334 | after | hardiness:susceptible | population replicate:1 |
| SA005590 | 336 | after | hardiness:susceptible | population replicate:1 |
| SA005591 | 338 | after | hardiness:susceptible | population replicate:1 |
| SA005592 | 333 | after | hardiness:susceptible | population replicate:1 |
| SA005593 | 335 | after | hardiness:susceptible | population replicate:1 |
| SA005594 | 332 | after | hardiness:susceptible | population replicate:1 |
| SA005595 | 337 | after | hardiness:susceptible | population replicate:1 |
| SA005596 | 331 | after | hardiness:susceptible | population replicate:1 |
| SA005597 | 635 | after | hardiness:susceptible | population replicate:2 |
| SA005598 | 638 | after | hardiness:susceptible | population replicate:2 |
| SA005599 | 632 | after | hardiness:susceptible | population replicate:2 |
| SA005600 | 631 | after | hardiness:susceptible | population replicate:2 |
| SA005601 | 636 | after | hardiness:susceptible | population replicate:2 |
| SA005602 | 634 | after | hardiness:susceptible | population replicate:2 |
| SA005603 | 637 | after | hardiness:susceptible | population replicate:2 |
| SA005604 | 633 | after | hardiness:susceptible | population replicate:2 |
| SA005605 | 211 | before | hardiness:hardy | population replicate:1 |
| SA005606 | 212 | before | hardiness:hardy | population replicate:1 |
| SA005607 | 213 | before | hardiness:hardy | population replicate:1 |
| SA005608 | 214 | before | hardiness:hardy | population replicate:1 |
| SA005609 | 216 | before | hardiness:hardy | population replicate:1 |
| SA005610 | 218 | before | hardiness:hardy | population replicate:1 |
| SA005611 | 215 | before | hardiness:hardy | population replicate:1 |
| SA005612 | 217 | before | hardiness:hardy | population replicate:1 |
| SA005613 | 518 | before | hardiness:hardy | population replicate:2 |
| SA005614 | 515 | before | hardiness:hardy | population replicate:2 |
| SA005615 | 516 | before | hardiness:hardy | population replicate:2 |
| SA005616 | 517 | before | hardiness:hardy | population replicate:2 |
| SA005617 | 514 | before | hardiness:hardy | population replicate:2 |
| SA005618 | 511 | before | hardiness:hardy | population replicate:2 |
| SA005619 | 512 | before | hardiness:hardy | population replicate:2 |
| SA005620 | 513 | before | hardiness:hardy | population replicate:2 |
| SA005621 | 315 | before | hardiness:susceptible | population replicate:1 |
| SA005622 | 317 | before | hardiness:susceptible | population replicate:1 |
| SA005623 | 311 | before | hardiness:susceptible | population replicate:1 |
| SA005624 | 313 | before | hardiness:susceptible | population replicate:1 |
| SA005625 | 312 | before | hardiness:susceptible | population replicate:1 |
| SA005626 | 318 | before | hardiness:susceptible | population replicate:1 |
| SA005627 | 316 | before | hardiness:susceptible | population replicate:1 |
| SA005628 | 314 | before | hardiness:susceptible | population replicate:1 |
| SA005629 | 614 | before | hardiness:susceptible | population replicate:2 |
| SA005630 | 615 | before | hardiness:susceptible | population replicate:2 |
| SA005631 | 613 | before | hardiness:susceptible | population replicate:2 |
| SA005632 | 612 | before | hardiness:susceptible | population replicate:2 |
| SA005633 | 618 | before | hardiness:susceptible | population replicate:2 |
| SA005634 | 616 | before | hardiness:susceptible | population replicate:2 |
| SA005635 | 611 | before | hardiness:susceptible | population replicate:2 |
| SA005636 | 617 | before | hardiness:susceptible | population replicate:2 |
| SA005637 | 228 | during | hardiness:hardy | population replicate:1 |
| SA005638 | 221 | during | hardiness:hardy | population replicate:1 |
| SA005639 | 227 | during | hardiness:hardy | population replicate:1 |
| SA005640 | 222 | during | hardiness:hardy | population replicate:1 |
| SA005641 | 224 | during | hardiness:hardy | population replicate:1 |
| SA005642 | 226 | during | hardiness:hardy | population replicate:1 |
| SA005643 | 225 | during | hardiness:hardy | population replicate:1 |
| SA005644 | 223 | during | hardiness:hardy | population replicate:1 |
| SA005645 | 527 | during | hardiness:hardy | population replicate:2 |
| SA005646 | 524 | during | hardiness:hardy | population replicate:2 |
| SA005647 | 522 | during | hardiness:hardy | population replicate:2 |
| SA005648 | 525 | during | hardiness:hardy | population replicate:2 |
| SA005649 | 521 | during | hardiness:hardy | population replicate:2 |
| SA005650 | 528 | during | hardiness:hardy | population replicate:2 |
| SA005651 | 526 | during | hardiness:hardy | population replicate:2 |
| SA005652 | 523 | during | hardiness:hardy | population replicate:2 |
| SA005653 | 324 | during | hardiness:susceptible | population replicate:1 |
| SA005654 | 325 | during | hardiness:susceptible | population replicate:1 |
| SA005655 | 328 | during | hardiness:susceptible | population replicate:1 |
| SA005656 | 326 | during | hardiness:susceptible | population replicate:1 |
| SA005657 | 327 | during | hardiness:susceptible | population replicate:1 |
| SA005658 | 323 | during | hardiness:susceptible | population replicate:1 |
| SA005659 | 321 | during | hardiness:susceptible | population replicate:1 |
| SA005660 | 322 | during | hardiness:susceptible | population replicate:1 |
| SA005661 | 625 | during | hardiness:susceptible | population replicate:2 |
| SA005662 | 628 | during | hardiness:susceptible | population replicate:2 |
| SA005663 | 624 | during | hardiness:susceptible | population replicate:2 |
| SA005664 | 626 | during | hardiness:susceptible | population replicate:2 |
| SA005665 | 627 | during | hardiness:susceptible | population replicate:2 |
| SA005666 | 622 | during | hardiness:susceptible | population replicate:2 |
| SA005667 | 623 | during | hardiness:susceptible | population replicate:2 |
| SA005668 | 621 | during | hardiness:susceptible | population replicate:2 |
| Showing results 1 to 96 of 96 |
Collection:
| Collection ID: | CO000104 |
| Collection Summary: | Flies are snap-frozen in liquid nitrogen, counted into pools of 10, and stored at -80 degC until extraction. |
| Collection Protocol Filename: | Fly_rearing_and_sample_collection_24Sept2014.docx |
| Sample Type: | whole bodies |
| Collection Method: | Snap-freeze in liquid nitrogen |
| Collection Location: | University of Florida |
| Storage Conditions: | -80 degC |
| Collection Vials: | 2mL eppendorf tubes |
| Storage Vials: | 2mL eppendorf tubes |
Treatment:
| Treatment ID: | TR000122 |
| Treatment Summary: | Flies are exposed to 3h in an ice slurry, then allowed to recover at room temperature for 5min. |
| Treatment Protocol Filename: | Fly_rearing_and_sample_collection_24Sept2014.docx |
| Treatment: | abiotic - cold exposure, 3h in ice slurry |
| Treatment Dose: | ice slurry |
| Treatment Doseduration: | 3h |
| Animal Endp Tissue Coll List: | 10 whole flies/sample |
Sample Preparation:
| Sampleprep ID: | SP000117 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | sample_prep_protocol_24Sept2014.docx sample_spiking_protocol_24Sept2014.docx |
| Sampleprep Protocol Comments: | Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37: 911-7. |
| Processing Method: | lyophilization, homogenization, solvent extraction |
| Processing Storage Conditions: | store at -20C |
| Extraction Method: | modified Bligh and Dyer protocol |
| Extract Concentration Dilution: | 2:2:1.8 (methanol:chloroform:water) |
| Extract Storage: | -20C |
| Sample Resuspension: | Samples were re-suspended in 620 ?l buffer (100 mM potassium phosphate [pH 7.3], 0.1% sodium azide, 1 mM trimethylsilylproprionate [TMSP] in D2O) |
| Sample Spiking: | 6 internal standards (proline, ?-alanine, tyrosine, histidine, phosphocholine, and 3-hydroxykynurenine) added: 6 ?L of standards were added to a concentration of 2x the Chenomx-determined concentration for each metabolite |
Analysis:
| Analysis ID: | AN000169 |
| Laboratory Name: | Molecular Science Research Center (MSRC), Claflin University, Orangeburg, SC |
| Analysis Type: | NMR |
| Analysis Comments: | NMR: 1D presaturation 1H |
| Acquisition Date: | Summer 2012 |
| Acquisition Parameters File: | nmr_data_acquisition_and_processing_protocol.doc |
| Instrument Parameters File: | Cold_adaptation_in_Drosophila_melanogaster.zip |
| Software Version: | TOPSPIN 2.1 |
| Operator Name: | Miki Watanabe and Arezue Boroujerdi |
| Chromatography ID: | CH000116 |
| Num Factors: | 12 |
| Num Metabolites: | 39 |
| Analysis ID: | AN000170 |
| Laboratory Name: | Molecular Science Research Center (MSRC), Claflin University, Orangeburg, SC |
| Analysis Type: | NMR |
| Analysis Comments: | NMR: 2D 1H-13C HSQC |
| Acquisition Date: | Summer 2012 |
| Acquisition Parameters File: | nmr_data_acquisition_and_processing_protocol.doc |
| Instrument Parameters File: | Cold_adaptation_in_Drosophila_melanogaster.zip |
| Software Version: | TOPSPIN 2.1 |
| Operator Name: | Miki Watanabe and Arezue Boroujerdi |
| Chromatography ID: | CH000116 |
| Num Factors: | 12 |
NMR:
| NMR ID: | NM000036 |
| Analysis ID: | AN000169 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | -6958.1 |
| Standard Concentration: | 1 mM TMSP |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | Room Temperature 5-mm triple resonance probe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5 mm |
| Shimming Method: | topshim (automatic shimming) |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presaturation |
| Pulse Width: | 9.4-9.6 ?s |
| Power Level: | -1.00 dB |
| Receiver Gain: | 200 |
| Offset Frequency: | 3294.98 Hz |
| Presaturation Power Level: | 53.64 dB |
| Chemical Shift Ref Cpd: | TMSP |
| Temperature: | 298 K |
| Number Of Scans: | 120 |
| Dummy Scans: | 4 |
| Acquisition Time: | 2.9 s |
| Relaxation Delay: | 4 s |
| Spectral Width: | 16.0872 ppm |
| Num Data Points Acquired: | 65536 |
| Real Data Points: | 32768 |
| Line Broadening: | 0.3 Hz |
| Zero Filling: | 2x |
| Apodization: | exponential multiply (em) |
| Baseline Correction Method: | abs (automatic baseline correction with integration (1D)) |
| Chemical Shift Ref Std: | 0.00 ppm |
| NMR ID: | NM000037 |
| Analysis ID: | AN000170 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 2D 1H-13C HSQC |
| Field Frequency Lock: | -6958.1 |
| Standard Concentration: | 1 mM TMSP |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | Room Temperature 5-mm triple resonance probe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5 mm |
| Shimming Method: | topshim (automatic shimming) |
| Pulse Sequence: | HSQCEDETGPSISP2.2 |
| Pulse Width: | 9.4-9.6 ?s |
| Power Level: | f1 -1.00 dB, f2 -4.13 dB |
| Receiver Gain: | 2050 |
| Offset Frequency: | f2 3294.95 Hz, f1 14081.41 Hz |
| Chemical Shift Ref Cpd: | TMSP |
| Temperature: | 298 K |
| Number Of Scans: | 256 |
| Dummy Scans: | 256 |
| Acquisition Time: | f2 0.13317 s, f1 0.0083333 s |
| Relaxation Delay: | 1.5 s |
| Spectral Width: | f2 10.9888, f1 180.00 |
| Num Data Points Acquired: | f2 2048, f1 528 |
| Real Data Points: | f2 4096, f1 2048 |
| Line Broadening: | f2 1.0 Hz, f1 0.3 Hz |
| Zero Filling: | f2 1x, f1 4x |
| Apodization: | f2 QSINE, f1 QSINE |
| Chemical Shift Ref Std: | 0.00, 0.00 ppm |
