#METABOLOMICS WORKBENCH cmw@berkeley.edu_20140926_9984451_mwtab.txt DATATRACK_ID:157 TEXT OUTPUT STUDY_ID:ST000102 ANALYSIS_ID:AN000170 PROJECT_ID:PR000094 VERSION 1 CREATED_ON 10-02-2015 #PROJECT PR:PROJECT_TITLE Cold adaptation shapes the robustness of metabolic networks in Drosophila PR:PROJECT_TITLE melanogaster PR:PROJECT_TYPE Genetic study PR:PROJECT_SUMMARY Flies that had been selected for fast and slow recovery from a cold-coma (2 PR:PROJECT_SUMMARY replicates of each type) were sampled before, during (at the end of a 3h cold PR:PROJECT_SUMMARY exposure at 0 degC), and after 5 min recovery from cold exposure. We tested the PR:PROJECT_SUMMARY hypothesis that cold adaptation remodelled metabolic networks to make them more PR:PROJECT_SUMMARY robust to the effects of cold. PR:INSTITUTE University of Florida PR:DEPARTMENT Entomology and Nematology PR:LABORATORY Daniel A. Hahn PR:LAST_NAME Hahn PR:FIRST_NAME Daniel PR:EMAIL dahahn@ufl.edu PR:FUNDING_SOURCE NSF IOS-1051890 PR:PHONE - PR:ADDRESS - #STUDY ST:STUDY_TITLE Cold adaptation shapes the robustness of metabolic networks in Drosophila ST:STUDY_TITLE melanogaster ST:STUDY_TYPE Time course during cold exposure for four genetic lines of flies ST:STUDY_SUMMARY Metabolites of cold hardy versus cold susceptible flies were compared using N ST:STUDY_SUMMARY less than R-based metabolomics. We used 8 replicates per line (2 hardy lines, ST:STUDY_SUMMARY two susceptible lines), and sampled each line at three time points (before, ST:STUDY_SUMMARY during and after cold), giving rise to 96 samples total. ST:INSTITUTE University of Florida ST:DEPARTMENT Entomology and Nematology ST:LAST_NAME Williams ST:FIRST_NAME Caroline ST:EMAIL cmw@berkeley.edu ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 96 ST:PHONE - ST:ADDRESS - #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Drosophila melanogaster SU:TAXONOMY_ID 7227 SU:GENOTYPE_STRAIN Originating from same base population as Drosophila melanogaster genetic SU:GENOTYPE_STRAIN reference panel, selected for fast (hardy) and slow (susceptible) recovery from SU:GENOTYPE_STRAIN chill coma. SU:AGE_OR_AGE_RANGE 5-7 day-old adults (mated) SU:WEIGHT_OR_WEIGHT_RANGE 0.17-0.77mg SU:HEIGHT_OR_HEIGHT_RANGE NA SU:GENDER Female SU:ANIMAL_HOUSING 25 degC SU:ANIMAL_LIGHT_CYCLE 12L:12D SU:ANIMAL_FEED Standard cornmeal molasses medium SU:ANIMAL_WATER in diet only SU:SPECIES_GROUP Insect #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 231 time:after | hardiness:hardy | population replicate:1 mass(mg)=4.8 SUBJECT_SAMPLE_FACTORS - 232 time:after | hardiness:hardy | population replicate:1 mass(mg)=5 SUBJECT_SAMPLE_FACTORS - 233 time:after | hardiness:hardy | population replicate:1 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 234 time:after | hardiness:hardy | population replicate:1 mass(mg)=5.4 SUBJECT_SAMPLE_FACTORS - 235 time:after | hardiness:hardy | population replicate:1 mass(mg)=5.8 SUBJECT_SAMPLE_FACTORS - 236 time:after | hardiness:hardy | population replicate:1 mass(mg)=5.2 SUBJECT_SAMPLE_FACTORS - 237 time:after | hardiness:hardy | population replicate:1 mass(mg)=5.1 SUBJECT_SAMPLE_FACTORS - 238 time:after | hardiness:hardy | population replicate:1 mass(mg)=4.3 SUBJECT_SAMPLE_FACTORS - 531 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.5 SUBJECT_SAMPLE_FACTORS - 532 time:after | hardiness:hardy | population replicate:2 mass(mg)=4.2 SUBJECT_SAMPLE_FACTORS - 533 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 534 time:after | hardiness:hardy | population replicate:2 mass(mg)=4.1 SUBJECT_SAMPLE_FACTORS - 535 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 536 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.5 SUBJECT_SAMPLE_FACTORS - 537 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 538 time:after | hardiness:hardy | population replicate:2 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 331 time:after | hardiness:susceptible | population replicate:1 mass(mg)=6.9 SUBJECT_SAMPLE_FACTORS - 332 time:after | hardiness:susceptible | population replicate:1 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 333 time:after | hardiness:susceptible | population replicate:1 mass(mg)=5.6 SUBJECT_SAMPLE_FACTORS - 334 time:after | hardiness:susceptible | population replicate:1 mass(mg)=5.2 SUBJECT_SAMPLE_FACTORS - 335 time:after | hardiness:susceptible | population replicate:1 mass(mg)=5.8 SUBJECT_SAMPLE_FACTORS - 336 time:after | hardiness:susceptible | population replicate:1 mass(mg)=5.3 SUBJECT_SAMPLE_FACTORS - 337 time:after | hardiness:susceptible | population replicate:1 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 338 time:after | hardiness:susceptible | population replicate:1 mass(mg)=5.3 SUBJECT_SAMPLE_FACTORS - 631 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 632 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 633 time:after | hardiness:susceptible | population replicate:2 mass(mg)=7.1 SUBJECT_SAMPLE_FACTORS - 634 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6.3 SUBJECT_SAMPLE_FACTORS - 635 time:after | hardiness:susceptible | population replicate:2 mass(mg)=5.9 SUBJECT_SAMPLE_FACTORS - 636 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6.3 SUBJECT_SAMPLE_FACTORS - 637 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6.7 SUBJECT_SAMPLE_FACTORS - 638 time:after | hardiness:susceptible | population replicate:2 mass(mg)=6 SUBJECT_SAMPLE_FACTORS - 211 time:before | hardiness:hardy | population replicate:1 mass(mg)=1.7 SUBJECT_SAMPLE_FACTORS - 212 time:before | hardiness:hardy | population replicate:1 mass(mg)=2.1 SUBJECT_SAMPLE_FACTORS - 213 time:before | hardiness:hardy | population replicate:1 mass(mg)=2.5 SUBJECT_SAMPLE_FACTORS - 214 time:before | hardiness:hardy | population replicate:1 mass(mg)=2.8 SUBJECT_SAMPLE_FACTORS - 215 time:before | hardiness:hardy | population replicate:1 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 216 time:before | hardiness:hardy | population replicate:1 mass(mg)=2.8 SUBJECT_SAMPLE_FACTORS - 217 time:before | hardiness:hardy | population replicate:1 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 218 time:before | hardiness:hardy | population replicate:1 mass(mg)=3.3 SUBJECT_SAMPLE_FACTORS - 511 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 512 time:before | hardiness:hardy | population replicate:2 mass(mg)=4.2 SUBJECT_SAMPLE_FACTORS - 513 time:before | hardiness:hardy | population replicate:2 mass(mg)=4.5 SUBJECT_SAMPLE_FACTORS - 514 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 515 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.3 SUBJECT_SAMPLE_FACTORS - 516 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.5 SUBJECT_SAMPLE_FACTORS - 517 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.6 SUBJECT_SAMPLE_FACTORS - 518 time:before | hardiness:hardy | population replicate:2 mass(mg)=3.2 SUBJECT_SAMPLE_FACTORS - 311 time:before | hardiness:susceptible | population replicate:1 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 312 time:before | hardiness:susceptible | population replicate:1 mass(mg)=4 SUBJECT_SAMPLE_FACTORS - 313 time:before | hardiness:susceptible | population replicate:1 mass(mg)=4 SUBJECT_SAMPLE_FACTORS - 314 time:before | hardiness:susceptible | population replicate:1 mass(mg)=4.3 SUBJECT_SAMPLE_FACTORS - 315 time:before | hardiness:susceptible | population replicate:1 mass(mg)=3.8 SUBJECT_SAMPLE_FACTORS - 316 time:before | hardiness:susceptible | population replicate:1 mass(mg)=4.3 SUBJECT_SAMPLE_FACTORS - 317 time:before | hardiness:susceptible | population replicate:1 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 318 time:before | hardiness:susceptible | population replicate:1 mass(mg)=4.1 SUBJECT_SAMPLE_FACTORS - 611 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.6 SUBJECT_SAMPLE_FACTORS - 612 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.5 SUBJECT_SAMPLE_FACTORS - 613 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.4 SUBJECT_SAMPLE_FACTORS - 614 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4 SUBJECT_SAMPLE_FACTORS - 615 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.3 SUBJECT_SAMPLE_FACTORS - 616 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.5 SUBJECT_SAMPLE_FACTORS - 617 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.8 SUBJECT_SAMPLE_FACTORS - 618 time:before | hardiness:susceptible | population replicate:2 mass(mg)=4.5 SUBJECT_SAMPLE_FACTORS - 221 time:during | hardiness:hardy | population replicate:1 mass(mg)=4.8 SUBJECT_SAMPLE_FACTORS - 222 time:during | hardiness:hardy | population replicate:1 mass(mg)=4.9 SUBJECT_SAMPLE_FACTORS - 223 time:during | hardiness:hardy | population replicate:1 mass(mg)=5.3 SUBJECT_SAMPLE_FACTORS - 224 time:during | hardiness:hardy | population replicate:1 mass(mg)=4.9 SUBJECT_SAMPLE_FACTORS - 225 time:during | hardiness:hardy | population replicate:1 mass(mg)=5.1 SUBJECT_SAMPLE_FACTORS - 226 time:during | hardiness:hardy | population replicate:1 mass(mg)=4.9 SUBJECT_SAMPLE_FACTORS - 227 time:during | hardiness:hardy | population replicate:1 mass(mg)=4.9 SUBJECT_SAMPLE_FACTORS - 228 time:during | hardiness:hardy | population replicate:1 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 521 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.8 SUBJECT_SAMPLE_FACTORS - 522 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 523 time:during | hardiness:hardy | population replicate:2 mass(mg)=4.2 SUBJECT_SAMPLE_FACTORS - 524 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.6 SUBJECT_SAMPLE_FACTORS - 525 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.7 SUBJECT_SAMPLE_FACTORS - 526 time:during | hardiness:hardy | population replicate:2 mass(mg)=4 SUBJECT_SAMPLE_FACTORS - 527 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.5 SUBJECT_SAMPLE_FACTORS - 528 time:during | hardiness:hardy | population replicate:2 mass(mg)=3.9 SUBJECT_SAMPLE_FACTORS - 321 time:during | hardiness:susceptible | population replicate:1 mass(mg)=7 SUBJECT_SAMPLE_FACTORS - 322 time:during | hardiness:susceptible | population replicate:1 mass(mg)=7.7 SUBJECT_SAMPLE_FACTORS - 323 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.9 SUBJECT_SAMPLE_FACTORS - 324 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.5 SUBJECT_SAMPLE_FACTORS - 325 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.6 SUBJECT_SAMPLE_FACTORS - 326 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.7 SUBJECT_SAMPLE_FACTORS - 327 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.8 SUBJECT_SAMPLE_FACTORS - 328 time:during | hardiness:susceptible | population replicate:1 mass(mg)=5.7 SUBJECT_SAMPLE_FACTORS - 621 time:during | hardiness:susceptible | population replicate:2 mass(mg)=6.5 SUBJECT_SAMPLE_FACTORS - 622 time:during | hardiness:susceptible | population replicate:2 mass(mg)=6.2 SUBJECT_SAMPLE_FACTORS - 623 time:during | hardiness:susceptible | population replicate:2 mass(mg)=6.2 SUBJECT_SAMPLE_FACTORS - 624 time:during | hardiness:susceptible | population replicate:2 mass(mg)=5.7 SUBJECT_SAMPLE_FACTORS - 625 time:during | hardiness:susceptible | population replicate:2 mass(mg)=4.3 SUBJECT_SAMPLE_FACTORS - 626 time:during | hardiness:susceptible | population replicate:2 mass(mg)=6 SUBJECT_SAMPLE_FACTORS - 627 time:during | hardiness:susceptible | population replicate:2 mass(mg)=6.1 SUBJECT_SAMPLE_FACTORS - 628 time:during | hardiness:susceptible | population replicate:2 mass(mg)=5.5 #COLLECTION CO:COLLECTION_SUMMARY Flies are snap-frozen in liquid nitrogen, counted into pools of 10, and stored CO:COLLECTION_SUMMARY at -80 degC until extraction. CO:COLLECTION_PROTOCOL_FILENAME Fly_rearing_and_sample_collection_24Sept2014.docx CO:SAMPLE_TYPE whole bodies CO:COLLECTION_METHOD Snap-freeze in liquid nitrogen CO:COLLECTION_LOCATION University of Florida CO:STORAGE_CONDITIONS -80 degC CO:COLLECTION_VIALS 2mL eppendorf tubes CO:STORAGE_VIALS 2mL eppendorf tubes #TREATMENT TR:TREATMENT_SUMMARY Flies are exposed to 3h in an ice slurry, then allowed to recover at room TR:TREATMENT_SUMMARY temperature for 5min. TR:TREATMENT_PROTOCOL_FILENAME Fly_rearing_and_sample_collection_24Sept2014.docx TR:TREATMENT abiotic - cold exposure, 3h in ice slurry TR:TREATMENT_DOSE ice slurry TR:TREATMENT_DOSEDURATION 3h TR:ANIMAL_ENDP_TISSUE_COLL_LIST 10 whole flies/sample #SAMPLEPREP SP:SAMPLEPREP_PROTOCOL_FILENAME sample_prep_protocol_24Sept2014.docx;sample_spiking_protocol_24Sept2014.docx SP:SAMPLEPREP_PROTOCOL_COMMENTS Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and SP:SAMPLEPREP_PROTOCOL_COMMENTS purification. Can J Biochem Physiol 37: 911-7. SP:PROCESSING_METHOD lyophilization, homogenization, solvent extraction SP:PROCESSING_STORAGE_CONDITIONS store at -20C SP:EXTRACTION_METHOD modified Bligh and Dyer protocol SP:EXTRACT_STORAGE -20C SP:SAMPLE_RESUSPENSION Samples were re-suspended in 620 ?l buffer (100 mM potassium phosphate [pH 7.3], SP:SAMPLE_RESUSPENSION 0.1% sodium azide, 1 mM trimethylsilylproprionate [TMSP] in D2O) SP:SAMPLE_SPIKING 6 internal standards (proline, ?-alanine, tyrosine, histidine, phosphocholine, SP:SAMPLE_SPIKING and 3-hydroxykynurenine) added: 6 ?L of standards were added to a concentration SP:SAMPLE_SPIKING of 2x the Chenomx-determined concentration for each metabolite SP:SAMPLEPREP_SUMMARY - #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE - CH:INSTRUMENT_NAME - CH:COLUMN_NAME - #ANALYSIS AN:LABORATORY_NAME Molecular Science Research Center (MSRC), Claflin University, Orangeburg, SC AN:ANALYSIS_TYPE NMR AN:ACQUISITION_DATE Summer 2012 AN:ACQUISITION_PARAMETERS_FILE nmr_data_acquisition_and_processing_protocol.doc AN:SOFTWARE_VERSION TOPSPIN 2.1 AN:OPERATOR_NAME Miki Watanabe and Arezue Boroujerdi #NMR NM:INSTRUMENT_TYPE Bruker Avance III NM:NMR_EXPERIMENT_TYPE 2D 1H-13C HSQC NM:FIELD_FREQUENCY_LOCK -6958.1 NM:STANDARD_CONCENTRATION 1 mM TMSP NM:SPECTROMETER_FREQUENCY 700 MHz NM:NMR_PROBE Room Temperature 5-mm triple resonance probe NM:NMR_SOLVENT D2O NM:NMR_TUBE_SIZE 5 mm NM:SHIMMING_METHOD topshim (automatic shimming) NM:PULSE_SEQUENCE HSQCEDETGPSISP2.2 NM:PULSE_WIDTH 9.4-9.6 ?s NM:POWER_LEVEL f1 -1.00 dB, f2 -4.13 dB NM:RECEIVER_GAIN 2050 NM:OFFSET_FREQUENCY f2 3294.95 Hz, f1 14081.41 Hz NM:CHEMICAL_SHIFT_REF_CPD TMSP NM:TEMPERATURE 298 K NM:NUMBER_OF_SCANS 256 NM:DUMMY_SCANS 256 NM:ACQUISITION_TIME f2 0.13317 s, f1 0.0083333 s NM:RELAXATION_DELAY 1.5 s NM:SPECTRAL_WIDTH f2 10.9888, f1 180.00 NM:NUM_DATA_POINTS_ACQUIRED f2 2048, f1 528 NM:REAL_DATA_POINTS f2 4096, f1 2048 NM:LINE_BROADENING f2 1.0 Hz, f1 0.3 Hz NM:ZERO_FILLING f2 1x, f1 4x NM:APODIZATION f2 QSINE, f1 QSINE NM:CHEMICAL_SHIFT_REF_STD 0.00, 0.00 ppm NM:INSTRUMENT_NAME Bruker AvanceTM III #END