{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003501","ANALYSIS_ID":"AN005748","PROJECT_ID":"PR002147","VERSION":"1","CREATED_ON":"September 26, 2024, 4:43 pm"},

"PROJECT":{"PROJECT_TITLE":"TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism","PROJECT_TYPE":"Preclinical Mouse study","PROJECT_SUMMARY":"Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application.","INSTITUTE":"Denali Therapeutics","DEPARTMENT":"Development Sciences","LAST_NAME":"Suh","FIRST_NAME":"Jung","ADDRESS":"161 Oyster Point Blvd, South San Francisco, California, 94080, USA","EMAIL":"suh@dnli.com","PHONE":"+1 6507973837","FUNDING_SOURCE":"Denali Therapeutics","PUBLICATIONS":"https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1"},

"STUDY":{"STUDY_TITLE":"TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism","STUDY_SUMMARY":"Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). To better understand the molecular and functional changes associated with TREM2 signalling, we generated a TREM2 reporter mouse model and observed a gradual upregulation of reporter expression with increasing plaque proximity. Isolated microglia were sorted based on reporter expression and their transcriptomic profiles acquired in both wildtype and APP transgenic animals, allowing us to disentangle TREM2 versus pathology-specific effects. Bulk RNA sequencing highlighted TREM2 level-dependent changes in major immunometabolic pathways, with enrichment of genes in oxidative phosphorylation and cholesterol metabolism in microglia with increased TREM2 expression. To confirm these findings, we next analysed uptake of fluorodeoxyglucose (FDG) and examined metabolomic and lipidomic profiles. Again, independent of Aβ pathology, TREM2 expression correlated with uptake of FDG as well as increased cellular redox, energetics, and cholesterol homeostasis. Finally, we performed chronic treatment with a brain penetrant TREM2 agonist and identified a window of TREM2 expression where microglia are most responsive. Thus, our data provide novel insights into TREM2-mediated regulation of microglial metabolic function and informs current efforts to bring TREM2 agonists into clinical application.","INSTITUTE":"Denali Therapeutics","LAST_NAME":"Suh","FIRST_NAME":"Jung","ADDRESS":"161 Oyster Point Blvd, South San Francisco, California, 94080, USA","EMAIL":"suh@dnli.com","PHONE":"+1 6507973837","NUM_GROUPS":"5","TOTAL_SUBJECTS":"26","NUM_MALES":"26","STUDY_COMMENTS":"Release as soon as it is possible","PUBLICATIONS":"https://www.biorxiv.org/content/10.1101/2024.07.18.604115v1"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","AGE_OR_AGE_RANGE":"15 mo","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Pool_1",
"Sample ID":"HSA-000019615",
"Factors":{"genotype":"NA","condition":"NA","group":"NA","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_002","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_001","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_002","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_002"}
},
{
"Subject ID":"2_59_mid_WT",
"Sample ID":"HSA-000019571",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_003","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_009","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_003","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_003"}
},
{
"Subject ID":"12_63_mid_WT",
"Sample ID":"HSA-000019581",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_004","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_027","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_004","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_004"}
},
{
"Subject ID":"24_78_low_APP",
"Sample ID":"HSA-000019593",
"Factors":{"genotype":"APP","condition":"low","group":"low_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_005","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_017","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_005","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_005"}
},
{
"Subject ID":"10_62_mid_WT",
"Sample ID":"HSA-000019579",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_006","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_016","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_006","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_006"}
},
{
"Subject ID":"15_69_low_WT",
"Sample ID":"HSA-000019584",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_007","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_022","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_007","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_007"}
},
{
"Subject ID":"25_78_mid_APP",
"Sample ID":"HSA-000019594",
"Factors":{"genotype":"APP","condition":"mid","group":"mid_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_008","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_012","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_008","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_008"}
},
{
"Subject ID":"18_74_mid_APP",
"Sample ID":"HSA-000019587",
"Factors":{"genotype":"APP","condition":"mid","group":"mid_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_009","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_003","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_009","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_009"}
},
{
"Subject ID":"17_74_low_APP",
"Sample ID":"HSA-000019586",
"Factors":{"genotype":"APP","condition":"low","group":"low_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_010","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_004","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_010","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_010"}
},
{
"Subject ID":"8_61_high_APP",
"Sample ID":"HSA-000019577",
"Factors":{"genotype":"APP","condition":"high","group":"high_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_011","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_011","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_011","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_011"}
},
{
"Subject ID":"21_76_mid_WT",
"Sample ID":"HSA-000019590",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_012","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_020","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_012","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_012"}
},
{
"Subject ID":"14_65_mid_WT",
"Sample ID":"HSA-000019583",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_013","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_028","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_013","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_013"}
},
{
"Subject ID":"7_61_mid_APP",
"Sample ID":"HSA-000019576",
"Factors":{"genotype":"APP","condition":"mid","group":"mid_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_014","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_023","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_014","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_014"}
},
{
"Subject ID":"1_59_low_WT",
"Sample ID":"HSA-000019570",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_015","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_026","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_015","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_015"}
},
{
"Subject ID":"5_60_high_APP",
"Sample ID":"HSA-000019574",
"Factors":{"genotype":"APP","condition":"high","group":"high_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_016","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_007","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_016","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_016"}
},
{
"Subject ID":"22_77_low_WT",
"Sample ID":"HSA-000019591",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_017","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_010","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_017","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_017"}
},
{
"Subject ID":"Pool_2",
"Sample ID":"HSA-000019616",
"Factors":{"genotype":"NA","condition":"NA","group":"NA","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_018","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_014","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_018","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_018"}
},
{
"Subject ID":"23_77_mid_WT",
"Sample ID":"HSA-000019592",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_019","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_015","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_019","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_019"}
},
{
"Subject ID":"11_63_low_WT",
"Sample ID":"HSA-000019580",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_020","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_019","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_020","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_020"}
},
{
"Subject ID":"3_60_low_APP",
"Sample ID":"HSA-000019572",
"Factors":{"genotype":"APP","condition":"low","group":"low_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_021","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_008","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_021","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_021"}
},
{
"Subject ID":"26_78_high_APP",
"Sample ID":"HSA-000019595",
"Factors":{"genotype":"APP","condition":"high","group":"high_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_022","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_025","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_022","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_022"}
},
{
"Subject ID":"19_74_high_APP",
"Sample ID":"HSA-000019588",
"Factors":{"genotype":"APP","condition":"high","group":"high_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_023","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_013","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_023","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_023"}
},
{
"Subject ID":"9_62_low_WT",
"Sample ID":"HSA-000019578",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_024","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_002","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_024","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_024"}
},
{
"Subject ID":"6_61_low_APP",
"Sample ID":"HSA-000019575",
"Factors":{"genotype":"APP","condition":"low","group":"low_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_025","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_021","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_025","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_025"}
},
{
"Subject ID":"20_76_low_WT",
"Sample ID":"HSA-000019589",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_026","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_024","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_026","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_026"}
},
{
"Subject ID":"4_60_mid_APP",
"Sample ID":"HSA-000019573",
"Factors":{"genotype":"APP","condition":"mid","group":"mid_disease","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_027","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_006","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_027","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_027"}
},
{
"Subject ID":"13_65_low_WT",
"Sample ID":"HSA-000019582",
"Factors":{"genotype":"WT","condition":"low","group":"low_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_028","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_018","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_028","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_028"}
},
{
"Subject ID":"16_69_mid_WT",
"Sample ID":"HSA-000019585",
"Factors":{"genotype":"WT","condition":"mid","group":"mid_healthy","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_029","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_005","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_029","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_029"}
},
{
"Subject ID":"Pool_3",
"Sample ID":"HSA-000019617",
"Factors":{"genotype":"NA","condition":"NA","group":"NA","Sample source":"microglia"},
"Additional sample data":{"RAW_FILE_NAME(Raw Source Name.LP)":"20220209_BL_HEX-000330_Lipid_Pos_030","RAW_FILE_NAME(Raw Source Name.TG)":"20220324_BL_HEX-000330_TGs_Pos_029","RAW_FILE_NAME(Raw Source Name.MP)":"20220209_BL_HEX-000330_Met_Pos_030","RAW_FILE_NAME(Raw Source Name.MN)":"20220211_BL_HEX-000330_Met_Neg_030"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Microglia isolation was performed using the Magnetic-activated cell sorting (MACS) system (Miltenyi Biotec). No CD11b enrichment step was performed as the intrinsic mKate2 reporter is only expressed in TREM2 expressing (microglia) cells. Hence, fluorescence-activated cell sorting was performed based on the mKate2 fluorescence signal and sorted into low, mid and high expressing subpopulations, as a proxy for the TREM2 expression of individual cells.","SAMPLE_TYPE":"microglia","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Pellets from the sorted subpopulations were reconstituted on ice in 9:1 MeOH:water including internal standards, vortexed for 1 minute, and spun down for 5 minutes at 10,000 g. Supernatant was transferred to glass vial for analysis by LC-MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"For each analysis, 5 µL of sample was injected on a BEH amide 1.7 µm, 2.1×150 mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.40 mL/min at 40°C. Mobile phase A consisted of water with 10 mM ammonium formate + 0.1% formic acid. Mobile phase B consisted of acetonitrile with 0.1% formic acid. The gradient was programmed as follows: 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)","SOLVENT_A":"100% water; 10 mM ammonium formate; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic acid","FLOW_GRADIENT":"0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B","FLOW_RATE":"0.40 mL/min","COLUMN_TEMPERATURE":"40"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500+ Qtrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"curtain gas at 30 psi; collision gas was set at medium; ion spray voltage at 5500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V; and  collision cell exit potential at 12.5 V."},

"MS_METABOLITE_DATA":{
"Units":"log2(area)",

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(m/z)":"181","product (m/z)":"138.3"},{"Metabolite":"Theophylline","internal standard":"6C13-Phenylalanine","Expected RT":"1.7","precursor (m/z)":"181.1","product (m/z)":"124"},{"Metabolite":"Thiamine","internal standard":"13C3-Thiamine","Expected RT":"5.07","precursor (m/z)":"265","product (m/z)":"122"},{"Metabolite":"Threonine","internal standard":"N15C13-Glycine","Expected RT":"5.86","precursor (m/z)":"120","product (m/z)":"74"},{"Metabolite":"Trigonelline","internal standard":"Methionine-d3","Expected RT":"5.3","precursor (m/z)":"138.1","product (m/z)":"94.1"},{"Metabolite":"Trimethylamine-d9 N-oxide","internal standard":"NA","Expected RT":"4.17","precursor (m/z)":"85","product (m/z)":"66"},{"Metabolite":"Trimethylamine-N-oxide","internal standard":"Trimethylamine-d9 N-oxide","Expected RT":"4.07","precursor (m/z)":"76.1","product (m/z)":"58.1"},{"Metabolite":"Tryptophan","internal standard":"6C13-Phenylalanine","Expected RT":"4.73","precursor (m/z)":"205","product (m/z)":"146.1"},{"Metabolite":"Tyrosine","internal standard":"6C13-Phenylalanine","Expected RT":"5.4","precursor (m/z)":"182.1","product (m/z)":"136"},{"Metabolite":"Uracil","internal standard":"Palmitoylcarnitine-d3","Expected RT":"2.47","precursor (m/z)":"113","product (m/z)":"70"},{"Metabolite":"Ureidopropionic acid","internal standard":"Palmitoylcarnitine-d3","Expected RT":"3.24","precursor (m/z)":"133","product (m/z)":"115"},{"Metabolite":"Uric acid","internal standard":"1,3-15N2-Uric acid","Expected RT":"5.28","precursor (m/z)":"169.1","product (m/z)":"141"},{"Metabolite":"Uridine","internal standard":"13C5-Hypoxanthine","Expected RT":"3.91","precursor (m/z)":"245","product (m/z)":"113"},{"Metabolite":"Valerobetaine","internal standard":"Valerobetaine-d9","Expected RT":"3.96","precursor (m/z)":"160","product (m/z)":"101.1"},{"Metabolite":"Valerobetaine-d9","internal standard":"NA","Expected RT":"4.09","precursor (m/z)":"169.1","product (m/z)":"101.1"},{"Metabolite":"Valine","internal standard":"6C13-Phenylalanine","Expected RT":"5.37","precursor (m/z)":"118.1","product (m/z)":"55"},{"Metabolite":"Valine-d8","internal standard":"NA","Expected RT":"5.17","precursor (m/z)":"126","product (m/z)":"80.1"},{"Metabolite":"Xanthine","internal standard":"6C13-Phenylalanine","Expected RT":"4.23","precursor (m/z)":"153","product (m/z)":"110"},{"Metabolite":"Xanthosine","internal standard":"6C13-Phenylalanine","Expected RT":"5.03","precursor (m/z)":"285","product (m/z)":"153"}]
}

}