#METABOLOMICS WORKBENCH hwelhaven_20220421_093038_mwtab.txt DATATRACK_ID:3213 STUDY_ID:ST002147 ANALYSIS_ID:AN003516 PROJECT_ID:PR001360 VERSION 1 CREATED_ON April 21, 2022, 12:06 pm #PROJECT PR:PROJECT_TITLE Welhaven_JBMR_tissues PR:PROJECT_SUMMARY This experiment investigated metabolomic differences female musculoskeletal PR:PROJECT_SUMMARY tissues. PR:INSTITUTE Montana State University PR:LAST_NAME Welhaven PR:FIRST_NAME Hope PR:ADDRESS Culbertson Hall, 100 PR:EMAIL hwelhaven@gmail.com PR:PHONE 4066961526 PR:FUNDING_SOURCE National Science Foundation (CMMI 1554708, CMMI 2120239) and the National PR:FUNDING_SOURCE Institutes of Health (NIAMS R01AR073964, NIGMS P20GM103474, NIH R03AG068680 #STUDY ST:STUDY_TITLE Metabolomic differences detected in female C57BL/6 mice ST:STUDY_SUMMARY Mice were euthanized at 20 weeks of age, and humeri were obtained for ST:STUDY_SUMMARY metabolomic analyses. Once obtained, marrow was flushed in some humeri resulting ST:STUDY_SUMMARY in 3 sample types including whole bone, bone marrow, and isolated cortical bone. ST:STUDY_SUMMARY Metabolites were extracted and underwent LC-MS analysis using an Agilent LC 1290 ST:STUDY_SUMMARY coupled to an Agilent 6538 QTOF ST:INSTITUTE Montana State University ST:LAST_NAME Welhaven ST:FIRST_NAME Hope ST:ADDRESS Culbertson Hall, 100 ST:EMAIL hwelhaven@gmail.com ST:PHONE 4066961526 ST:NUM_GROUPS 3 ST:TOTAL_SUBJECTS 10 ST:NUM_FEMALES 10 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENOTYPE_STRAIN C57Bl/6 SU:AGE_OR_AGE_RANGE 20 weeks (at euthanasia) SU:GENDER Female SU:ANIMAL_ANIMAL_SUPPLIER Jackson Labratories SU:ANIMAL_LIGHT_CYCLE Standard light dark cycle SU:ANIMAL_FEED PicoLab Rodent Diet 20, 20% protein #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - MV1 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_1 SUBJECT_SAMPLE_FACTORS - MV2 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_2 SUBJECT_SAMPLE_FACTORS - MV3 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_3 SUBJECT_SAMPLE_FACTORS - MV4 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_4 SUBJECT_SAMPLE_FACTORS - MV5 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_5 SUBJECT_SAMPLE_FACTORS - MV6 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_6 SUBJECT_SAMPLE_FACTORS - MV7 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_7 SUBJECT_SAMPLE_FACTORS - MV8 Sex:F | Tissue:isolated_bone RAW_FILE_NAME=Welhaven_isolatedbone_8 SUBJECT_SAMPLE_FACTORS - MV9 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_9 SUBJECT_SAMPLE_FACTORS - MV10 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_10 SUBJECT_SAMPLE_FACTORS - MV11 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_11 SUBJECT_SAMPLE_FACTORS - MV12 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_12 SUBJECT_SAMPLE_FACTORS - MV13 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_13 SUBJECT_SAMPLE_FACTORS - MV14 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_14 SUBJECT_SAMPLE_FACTORS - MV15 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_15 SUBJECT_SAMPLE_FACTORS - MV16 Sex:F | Tissue:whole_bone RAW_FILE_NAME=Welhaven_wholebone_16 SUBJECT_SAMPLE_FACTORS - MV17 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_17 SUBJECT_SAMPLE_FACTORS - MV18 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_18 SUBJECT_SAMPLE_FACTORS - MV19 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_19 SUBJECT_SAMPLE_FACTORS - MV20 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_20 SUBJECT_SAMPLE_FACTORS - MV21 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_21 SUBJECT_SAMPLE_FACTORS - MV22 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_22 SUBJECT_SAMPLE_FACTORS - MV23 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_23 SUBJECT_SAMPLE_FACTORS - MV24 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_24 SUBJECT_SAMPLE_FACTORS - MV25 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_25 SUBJECT_SAMPLE_FACTORS - MV26 Sex:F | Tissue:bone_marrow RAW_FILE_NAME=Welhaven_bonemarrow_26 #COLLECTION CO:COLLECTION_SUMMARY Samples were collected following mouse euthanasia. The humerus was obtained and CO:COLLECTION_SUMMARY bone marrow was flushed resulting in 3 groups: isolated bone, bone marrow, and CO:COLLECTION_SUMMARY whole bone (has intact marrow). CO:SAMPLE_TYPE Bone and bone marrow #TREATMENT TR:TREATMENT_SUMMARY Mice were housed at Montana State University after being obtained from Jackson TR:TREATMENT_SUMMARY labs. During this time, mice were kept on a light/dark cycle and fed a standard TR:TREATMENT_SUMMARY chow diet ad libitum. Upon 20 weeks of age, mice were euthanized. No additional TR:TREATMENT_SUMMARY factors such as injury, diet, or exercise occurred. Mice were simply used to TR:TREATMENT_SUMMARY analyze differences in metabolism between musculoskeletal tissues. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Once euthanized, tissues were dissected and harvested. Samples underwent a SP:SAMPLEPREP_SUMMARY methanol:acetone extraction and underwent rounds of centrifugation. Once SP:SAMPLEPREP_SUMMARY metabolites were isolated, samples were dried via vacuum concentration and SP:SAMPLEPREP_SUMMARY resuspended with acetonitrile:water for LC-MS analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Samples were analyzed using an Agilent 1290 UPLC coupled to an Agilent 6538 CH:CHROMATOGRAPHY_SUMMARY QTOF. All samples were run in normal phase using a Cogent Diamond Hydride HILIC CH:CHROMATOGRAPHY_SUMMARY column (150 x 2.1 mm). Solvents: 0.1% formic acid in water (A), 0.1% formic acid CH:CHROMATOGRAPHY_SUMMARY in acetonitrile (B). Elution gradient: 100 to 25% solvent B over 17 minutes, 0 CH:CHROMATOGRAPHY_SUMMARY to 70% solvent A over 20 minutes, at 21 minutes, B increases from 25% to 100% CH:CHROMATOGRAPHY_SUMMARY till 25 minutes while A decreases from 70% to 0% till 25 minutes. The last 4 CH:CHROMATOGRAPHY_SUMMARY minutes act as a wash. Total run time = 25 minute method (per sample) CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 6538 CH:COLUMN_NAME Cogent Diamond Hydride HILIC 150 × 2.1 mm column #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6538 QTOF MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS - MS:MS_RESULTS_FILE ST002147_AN003516_Results.txt UNITS:Peak Intensiy Has m/z:Yes Has RT:No RT units:No RT data #END