#METABOLOMICS WORKBENCH araskind_20170619_180227 DATATRACK_ID:1040 STUDY_ID:ST000737 ANALYSIS_ID:AN001151 PROJECT_ID:PR000533 VERSION 1 CREATED_ON July 3, 2017, 1:12 pm #PROJECT PR:PROJECT_TITLE Metabolic change in macrophages after efferocytosis PR:PROJECT_TYPE MS analysis PR:PROJECT_SUMMARY To study metabolic change in macrophages after efferocytosis PR:INSTITUTE Northwestern University PR:DEPARTMENT Pathology PR:LABORATORY Thorp Lab PR:LAST_NAME Thorp PR:FIRST_NAME Edward PR:ADDRESS Evanston, IL PR:EMAIL ebthorp@northwestern.edu PR:PHONE 312-503-4309 #STUDY ST:STUDY_TITLE Metabolic change in macrophages after efferocytosis (part II) ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY The goal of the experiment is to study metabolic pathway alteration in ST:STUDY_SUMMARY macrophages after efferocytosis (when macrophages eating apoptotic cells). ST:STUDY_SUMMARY Peritoneal macrophages were purified and plated in the cell-culture dishes. ST:STUDY_SUMMARY After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 ST:STUDY_SUMMARY hours, then un-engulfed cells were removed through washing. Macrophages were ST:STUDY_SUMMARY left in the plate for another 4 hours before being lifted from the plate. ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@med.umich.edu ST:PHONE (734) 232-8175 ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 1 #SUBJECT SU:SUBJECT_TYPE Mouse SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0015592 S00024013 Treatment:none SUBJECT_SAMPLE_FACTORS SU0015592 S00024014 Treatment:none SUBJECT_SAMPLE_FACTORS SU0015592 S00024015 Treatment:apoptotic cells for 2hrs SUBJECT_SAMPLE_FACTORS SU0015592 S00024016 Treatment:apoptotic cells for 2hrs SUBJECT_SAMPLE_FACTORS SU0015592 S00024017 Treatment:apoptotic cells for 2hrs SUBJECT_SAMPLE_FACTORS SU0015592 S00024018 Treatment:ko untreated SUBJECT_SAMPLE_FACTORS SU0015592 S00024019 Treatment:ko untreated SUBJECT_SAMPLE_FACTORS SU0015592 S00024020 Treatment:ko treated with apoptotic cells 2hrs SUBJECT_SAMPLE_FACTORS SU0015592 S00024021 Treatment:ko treated with apoptotic cells 2hrs SUBJECT_SAMPLE_FACTORS SU0015592 S00024022 Treatment:ko treated with apoptotic cells 2hrs #COLLECTION CO:COLLECTION_SUMMARY - #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME A011 - Glycolysis-TCA-nucleotides.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent 7890N CH:COLUMN_NAME Agilent HP5-MS (15m × 0.25mm, 0.25 um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A011 - Glycolysis-TCA-nucleotides.pdf #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 5975 MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE EI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/ug protein MS_METABOLITE_DATA_START Samples S00024013 S00024014 S00024015 S00024016 S00024017 S00024018 S00024019 S00024020 S00024021 S00024022 Factors Treatment:none Treatment:none Treatment:apoptotic cells for 2hrs Treatment:apoptotic cells for 2hrs Treatment:apoptotic cells for 2hrs Treatment:ko untreated Treatment:ko untreated Treatment:ko treated with apoptotic cells 2hrs Treatment:ko treated with apoptotic cells 2hrs Treatment:ko treated with apoptotic cells 2hrs D-ERYTHROSE 4-PHOSPHATE .00106586 0 .001958876 .001292215 0 .007599994 .008146643 .003979795 .005497746 .003390573 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) .003890481 .001945037 .005114715 .002222935 .004980454 .008437272 .006940036 .007476818 .006812015 .008952233 CITRIC ACID .020915117 .017025853 .021440712 .028471986 .017258225 .065730765 .069203622 .071994548 .054862786 .037426972 FAD 0 0 0 0 0 0 0 .0000348907 .000044205 0 MALIC ACID .012652249 .011595965 .024237432 .034194884 .021873915 .032693286 .044060541 .039575982 .037726584 .031340399 ADENOSINE TRIPHOSPHATE .002151351 .00204589 .002234721 .002060296 .002174957 .003671275 .003597657 .002302726 .001890725 .002201398 ROBISON ESTER .005113045 .003987889 .00426487 .003153601 .002516779 .006615638 .020124577 .008297248 .008095753 .00623114 SUCROSE 0 0 0 0 0 .001716088 .002007621 .012244551 .014661049 .008125526 ADENOSINE 5'-DIPHOSPHATE .002222532 .00201846 .002886605 .002735473 .003192554 .005605718 .00544571 .005237412 .003537134 .004722127 ADENOSINE 5'-MONOPHOSPHATE .006053719 .003565046 .003834798 .003334564 .006877784 .013749327 .014710731 .013603214 .004438048 .012762911 GLYCERATE 3-PHOSPHATE 0 0 0 0 0 .000232519 0 0 0 0 RIBOSE PHOSPHATE .006054687 .007080436 .01366128 .015745723 .007121562 .012813887 .014748332 .013491506 .021274454 .010218364 6-PHOSPHOGLUCONIC ACID .001497523 .001529843 .001540677 .001544017 .001526052 .002816493 .002646342 .001274555 .001234628 .001294086 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type D-ERYTHROSE 4-PHOSPHATE 122357 D-FRUCTOSE, 1,6-BIS(DIHYDROGEN PHOSPHATE) 21125049 CITRIC ACID 311 FAD 46906035 MALIC ACID 525 ADENOSINE TRIPHOSPHATE 5957 ROBISON ESTER 5958 SUCROSE 5988 ADENOSINE 5'-DIPHOSPHATE 6022 ADENOSINE 5'-MONOPHOSPHATE 6083 GLYCERATE 3-PHOSPHATE 724 RIBOSE PHOSPHATE 77982 6-PHOSPHOGLUCONIC ACID 91493 METABOLITES_END #END