#METABOLOMICS WORKBENCH araskind_20170619_180044 DATATRACK_ID:1039 STUDY_ID:ST000736 ANALYSIS_ID:AN001150 PROJECT_ID:PR000533 VERSION 1 CREATED_ON July 3, 2017, 12:32 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 ST:STUDY_TYPE MS analysis ST:STUDY_SUMMARY Study metabolic pathway alteration in macrophages after efferocytosis (when ST:STUDY_SUMMARY macrophages eating apoptotic cells). Peritoneal macrophages were purified and ST:STUDY_SUMMARY plated in the cell-culture dishes. After culturing overnight. Apoptotic cells ST:STUDY_SUMMARY were overlayed to macrophages for 2 hours, then un-engulfed cells were removed ST:STUDY_SUMMARY through washing. Macrophages were left in the plate for another 4 hours before ST:STUDY_SUMMARY 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 5 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 SU0013786 S00020913 Treatment:none SUBJECT_SAMPLE_FACTORS SU0013786 S00020914 Treatment:none SUBJECT_SAMPLE_FACTORS SU0013786 S00020915 Treatment:apoptotic cells for 2 hours SUBJECT_SAMPLE_FACTORS SU0013786 S00020916 Treatment:apoptotic cells for 2 hours SUBJECT_SAMPLE_FACTORS SU0013786 S00020917 Treatment:apoptotic cells for 2 hours SUBJECT_SAMPLE_FACTORS SU0013786 S00020918 Treatment:ko untreated SUBJECT_SAMPLE_FACTORS SU0013786 S00020919 Treatment:ko untreated SUBJECT_SAMPLE_FACTORS SU0013786 S00020920 Treatment:ko treated with apoptotic cells 2hrs SUBJECT_SAMPLE_FACTORS SU0013786 S00020921 Treatment:ko treated with apoptotic cells 2 hrs SUBJECT_SAMPLE_FACTORS SU0013786 S00020922 Treatment:ko treated with apoptotic cells 2 hrs #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 HILIC CH:INSTRUMENT_NAME Agilent CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) #ANALYSIS AN:ANALYSIS_TYPE MS AN:ANALYSIS_PROTOCOL_FILE A011 - Glycolysis-TCA-nucleotides.pdf #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6520B QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS counts MS_METABOLITE_DATA_START Samples S00020913 S00020914 S00020915 S00020916 S00020917 S00020918 S00020919 S00020920 S00020921 S00020922 Factors Treatment:none Treatment:none Treatment:apoptotic cells for 2 hours Treatment:apoptotic cells for 2 hours Treatment:apoptotic cells for 2 hours Treatment:ko untreated Treatment:ko untreated Treatment:ko treated with apoptotic cells 2hrs Treatment:ko treated with apoptotic cells 2 hrs Treatment:ko treated with apoptotic cells 2 hrs XANTHINE 105151 63757 579974 578715 535447 340657 373986 780294 874081 642803 HEXOPYRANOSE 259377 341640 666318 573966 596058 272018 252238 791756 725652 771341 CITRIC ACID 8583517 6624953 7639874 5929683 8642758 6586761 6147650 9970224 6042404 7047741 DL-ASPARTIC ACID 4864664 4889908 3883201 4000330 2651796 2822236 2557041 3986783 3052645 2907860 OLEIC ACID 4231990 4697056 7536088 7587419 6995680 6676446 4950031 10692288 11600169 11426963 STEARIC ACID 20016122 15371109 17579309 17040678 13046999 20230254 15859216 18243587 15276115 17189468 ADENOSINE TRIPHOSPHATE 2660912 3309513 4112698 385391 2342068 265312 443067 2149398 82945 555266 L-GLUTAMINE 885575 811857 3081781 2640518 2715004 568768 548955 2923350 2303232 2323019 L-LYSINE 49088 41239 285413 276431 296903 52314 39772 348265 293363 330699 ADENOSINE 5'-DIPHOSPHATE 4633774 4214840 3280832 2147441 3179734 1866116 2738734 4727528 1195479 3627633 DL-GLUTAMIC ACID 6941086 7913602 12005280 13170253 9894104 7591595 7223025 15540686 11240652 10767160 LACTIC ACID 3994 36936 8542 47451 59229 62827 2071 93600 3358 52449 GLYCERALDEHYDE 3-PHOSPHATE 2429 5218 7013 11021 17392 3240 2241 15329 8232 13605 HYPOXANTHINE 536277 656057 625438 603619 467856 440921 345946 662032 476493 439799 ACETOACETYL-COA 40934 38569 14512 11088 19702 20261 19872 19302 7097 7194 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 XANTHINE 1188 HEXOPYRANOSE 206 CITRIC ACID 311 DL-ASPARTIC ACID 424 OLEIC ACID 445639 STEARIC ACID 5281 ADENOSINE TRIPHOSPHATE 5957 L-GLUTAMINE 5961 L-LYSINE 5962 ADENOSINE 5'-DIPHOSPHATE 6022 DL-GLUTAMIC ACID 611 LACTIC ACID 612 GLYCERALDEHYDE 3-PHOSPHATE 729 HYPOXANTHINE 790 ACETOACETYL-COA 92153 METABOLITES_END #END