{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000102","ANALYSIS_ID":"AN000169","VERSION":"1","CREATED_ON":"08-08-2023"},

"PROJECT":{"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","DOI":"http://dx.doi.org/10.21228/M8X309"},

"STUDY":{"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","EMAIL":"cmw@berkeley.edu","SUBMIT_DATE":"2014-09-26"},

"SUBJECT":{"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"},
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"Subject ID":"-",
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"Additional sample data":{"mass(mg)":"5"}
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"Subject ID":"-",
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"Subject ID":"-",
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{
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"Subject ID":"-",
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{
"Subject ID":"-",
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{
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{
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},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"1"},
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},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"1"},
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},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"1"},
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{
"Subject ID":"-",
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{
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},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"1"},
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},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"1"},
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},
{
"Subject ID":"-",
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"Additional sample data":{"mass(mg)":"6.5"}
},
{
"Subject ID":"-",
"Sample ID":"622",
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},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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"Additional sample data":{"mass(mg)":"6"}
},
{
"Subject ID":"-",
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"Factors":{"time":"during","hardiness":"susceptible","population replicate":"2"},
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},
{
"Subject ID":"-",
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}
],
"COLLECTION":{"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_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"},

"SAMPLEPREP":{"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_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":[],

"ANALYSIS":{"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"},

"NM":{"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"},

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}