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.

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Study IDST000102
Study TitleCold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster
Study TypeTime course during cold exposure for four genetic lines of flies
Study SummaryMetabolites 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
DepartmentEntomology and Nematology
Last NameWilliams
First NameCaroline
Emailcmw@berkeley.edu
Submit Date2014-09-26
Num Groups4
Total Subjects96
Raw Data AvailableYes
Raw Data File Type(s).txt,out, .xml, .par, pdata directory has binary files
Uploaded File Size151 M
Analysis Type DetailNMR
Release Date2015-02-03
Release Version1
Caroline Williams Caroline Williams
https://dx.doi.org/10.21228/M8X309
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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 hardiness population replicate
SA005573238after hardy 1
SA005574231after hardy 1
SA005575232after hardy 1
SA005576237after hardy 1
SA005577236after hardy 1
SA005578234after hardy 1
SA005579235after hardy 1
SA005580233after hardy 1
SA005581531after hardy 2
SA005582536after hardy 2
SA005583538after hardy 2
SA005584533after hardy 2
SA005585537after hardy 2
SA005586535after hardy 2
SA005587534after hardy 2
SA005588532after hardy 2
SA005589334after susceptible 1
SA005590336after susceptible 1
SA005591338after susceptible 1
SA005592333after susceptible 1
SA005593335after susceptible 1
SA005594332after susceptible 1
SA005595337after susceptible 1
SA005596331after susceptible 1
SA005597635after susceptible 2
SA005598638after susceptible 2
SA005599632after susceptible 2
SA005600631after susceptible 2
SA005601636after susceptible 2
SA005602634after susceptible 2
SA005603637after susceptible 2
SA005604633after susceptible 2
SA005605211before hardy 1
SA005606212before hardy 1
SA005607213before hardy 1
SA005608214before hardy 1
SA005609216before hardy 1
SA005610218before hardy 1
SA005611215before hardy 1
SA005612217before hardy 1
SA005613518before hardy 2
SA005614515before hardy 2
SA005615516before hardy 2
SA005616517before hardy 2
SA005617514before hardy 2
SA005618511before hardy 2
SA005619512before hardy 2
SA005620513before hardy 2
SA005621315before susceptible 1
SA005622317before susceptible 1
SA005623311before susceptible 1
SA005624313before susceptible 1
SA005625312before susceptible 1
SA005626318before susceptible 1
SA005627316before susceptible 1
SA005628314before susceptible 1
SA005629614before susceptible 2
SA005630615before susceptible 2
SA005631613before susceptible 2
SA005632612before susceptible 2
SA005633618before susceptible 2
SA005634616before susceptible 2
SA005635611before susceptible 2
SA005636617before susceptible 2
SA005637228during hardy 1
SA005638221during hardy 1
SA005639227during hardy 1
SA005640222during hardy 1
SA005641224during hardy 1
SA005642226during hardy 1
SA005643225during hardy 1
SA005644223during hardy 1
SA005645527during hardy 2
SA005646524during hardy 2
SA005647522during hardy 2
SA005648525during hardy 2
SA005649521during hardy 2
SA005650528during hardy 2
SA005651526during hardy 2
SA005652523during hardy 2
SA005653324during susceptible 1
SA005654325during susceptible 1
SA005655328during susceptible 1
SA005656326during susceptible 1
SA005657327during susceptible 1
SA005658323during susceptible 1
SA005659321during susceptible 1
SA005660322during susceptible 1
SA005661625during susceptible 2
SA005662628during susceptible 2
SA005663624during susceptible 2
SA005664626during susceptible 2
SA005665627during susceptible 2
SA005666622during susceptible 2
SA005667623during susceptible 2
SA005668621during susceptible 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 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

Chromatography:

Chromatography ID:CH000116

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
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