{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000657","ANALYSIS_ID":"AN001003","VERSION":"1","CREATED_ON":"June 28, 2017, 11:01 am"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics analysis of different mouse APC subsets from lung and spleen of WT and mTOR-APC-KO","PROJECT_SUMMARY":"Antigen presenting cells from WT or mTOR-APC-KO mice were sorted from lung and spleens and subjected to metabolomics analysis.","INSTITUTE":"Emory University","DEPARTMENT":"Department of Medicine","LABORATORY":"Clinical Biomarkers Laboratory","LAST_NAME":"Li; Gardinassi","FIRST_NAME":"Shuzhao; Luiz","ADDRESS":"Whitehead Biomedical Research Building, Suit 205, 615 Michael Street, Atlanta, GA 30322","EMAIL":"shuzhao.li@gmail.com or luiz.gardinassi@emory.edu","PHONE":"404-712-2988"},

"STUDY":{"STUDY_TITLE":"mTOR regulates metabolic adaptation of APCs in the lung microenvironment and controls the outcome of allergic inflammation","STUDY_SUMMARY":"Antigen presenting cells (APCs) occupy diverse anatomical tissues, but their tissue-restricted homeostasis remains poorly understood. Here, working in mouse models of inflammation, we found that mTOR-dependent metabolic adaptation was required at discrete locations. mTOR was dispensable for DC homeostasis in secondary lymphoid tissues, but necessary to regulate cellular metabolism and accumulation of CD103+ DCs and alveolar macrophages in lung. Moreover, whilst numbers of mTOR-deficient lung CD11b+ DCs were not changed, they were metabolically reprogrammed to skew allergic inflammation from eosinophilic Th2 to neutrophilic Th17 polarity. The mechanism for this change was independent of translational control, but dependent on inflammatory DC which produced IL-23 and increased fatty acid oxidation. mTOR therefore mediates metabolic adaptation of APCs in distinct tissues, influencing the immunological character of allergic inflammation.","INSTITUTE":"Emory University","LAST_NAME":"Li; Gardinassi","FIRST_NAME":"Shuzhao; Luiz","ADDRESS":"Emory Woodruff Memorial Research Building, 1639 Pierce Dr NE, Atlanta, GA 30322","EMAIL":"shuzhao.li@gmail.com; luiz.gardinassi@emory.edu","PHONE":"404-712-2988 or 404-727-5091"},

"SUBJECT":{"SUBJECT_TYPE":"cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"WT or mTOR-APC-KO/C57BL6"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"1162014_CD8a_Spleen_B6_1",
"Sample ID":"VT_150922_001",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a_Spleen_B6_3",
"Sample ID":"VT_150922_003",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a_Spleen_B6_5",
"Sample ID":"VT_150922_005",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 2_Spleen_B6_1",
"Sample ID":"VT_150922_007",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 2_Spleen_B6_3",
"Sample ID":"VT_150922_009",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 2_Spleen_B6_5",
"Sample ID":"VT_150922_011",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 3_Spleen_B6_1",
"Sample ID":"VT_150922_013",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 3_Spleen_B6_3",
"Sample ID":"VT_150922_015",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD8a 3_Spleen_B6_5",
"Sample ID":"VT_150922_017",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD8a_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_019",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD8a_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_021",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD8a_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_023",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 1_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_025",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 1_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_027",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 1_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_029",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 2_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_031",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 2_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_033",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD8a 2_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_035",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b_Spleen_B6_1",
"Sample ID":"VT_150922_037",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b_Spleen_B6_3",
"Sample ID":"VT_150922_039",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b_Spleen_B6_5",
"Sample ID":"VT_150922_041",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 2_Spleen_B6_1",
"Sample ID":"VT_150922_043",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 2_Spleen_B6_3",
"Sample ID":"VT_150922_045",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 2_Spleen_B6_5",
"Sample ID":"VT_150922_047",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 3_Spleen_B6_1",
"Sample ID":"VT_150922_049",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 3_Spleen_B6_3",
"Sample ID":"VT_150922_051",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1162014_CD11b 3_Spleen_B6_5",
"Sample ID":"VT_150922_053",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_055",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_057",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_059",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 1_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_061",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 1_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_063",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 1_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_065",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 2_Spleen_mTOR DC-KO_1",
"Sample ID":"VT_150922_067",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 2_Spleen_mTOR DC-KO_3",
"Sample ID":"VT_150922_069",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b 2_Spleen_mTOR DC-KO_5",
"Sample ID":"VT_150922_071",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 1_Lung_B6_1",
"Sample ID":"VT_150922_073",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 1_Lung_B6_3",
"Sample ID":"VT_150922_075",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 1_Lung_B6_5",
"Sample ID":"VT_150922_077",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 2_Lung_B6_1",
"Sample ID":"VT_150922_079",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 2_Lung_B6_3",
"Sample ID":"VT_150922_081",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_AM 2_Lung_B6_5",
"Sample ID":"VT_150922_083",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_AM 1_Lung_B6_1",
"Sample ID":"VT_150922_085",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_AM 1_Lung_B6_3",
"Sample ID":"VT_150922_087",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_AM 1_Lung_B6_5",
"Sample ID":"VT_150922_089",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM A_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_091",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM A_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_093",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM A_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_095",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM B_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_097",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM B_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_099",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_AM B_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_101",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_AM A_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_103",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_AM A_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_105",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_AM A_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_107",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD11b_Lung_B6_1",
"Sample ID":"VT_150922_109",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD11b_Lung_B6_3",
"Sample ID":"VT_150922_111",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD11b_Lung_B6_5",
"Sample ID":"VT_150922_113",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 1_Lung_B6_1",
"Sample ID":"VT_150922_115",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 1_Lung_B6_3",
"Sample ID":"VT_150922_117",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 1_Lung_B6_5",
"Sample ID":"VT_150922_119",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 2_Lung_B6_1",
"Sample ID":"VT_150922_121",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 2_Lung_B6_3",
"Sample ID":"VT_150922_123",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD11b 2_Lung_B6_5",
"Sample ID":"VT_150922_125",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b A_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_127",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b A_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_129",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b A_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_131",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b B_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_133",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b B_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_135",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD11b B_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_137",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b B_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_139",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b B_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_141",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD11b B_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_143",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD103_Lung_B6_1",
"Sample ID":"VT_150922_145",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD103_Lung_B6_3",
"Sample ID":"VT_150922_147",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"10162014_CD103_Lung_B6_5",
"Sample ID":"VT_150922_149",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 1_Lung_B6_1",
"Sample ID":"VT_150922_151",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 1_Lung_B6_3",
"Sample ID":"VT_150922_153",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 1_Lung_B6_5",
"Sample ID":"VT_150922_155",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 2_Lung_B6_1",
"Sample ID":"VT_150922_157",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 2_Lung_B6_3",
"Sample ID":"VT_150922_159",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"1132014_CD103 2_Lung_B6_5",
"Sample ID":"VT_150922_161",
"Factors":{"Genotype":"WT","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD103+ A&B_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_163",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD103+ A&B_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_165",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"12172014_CD103+ A&B_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_167",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD103+ A&B_Lung_mTOR DC-KO_1",
"Sample ID":"VT_150922_169",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD103+ A&B_Lung_mTOR DC-KO_3",
"Sample ID":"VT_150922_171",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"162014_CD103+ A&B_Lung_mTOR DC-KO_5",
"Sample ID":"VT_150922_173",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"No"}
},
{
"Subject ID":"3192015_DC WT 1_HDM Lung_mTOR ctrl_1",
"Sample ID":"VT_150922_175",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 1_HDM Lung_mTOR ctrl_3",
"Sample ID":"VT_150922_177",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 1_HDM Lung_mTOR ctrl_5",
"Sample ID":"VT_150922_179",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 2_HDM Lung_mTOR ctrl_1",
"Sample ID":"VT_150922_181",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 2_HDM Lung_mTOR ctrl_3",
"Sample ID":"VT_150922_183",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 2_HDM Lung_mTOR ctrl_5",
"Sample ID":"VT_150922_185",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 3_HDM Lung_mTOR ctrl_1",
"Sample ID":"VT_150922_187",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 3_HDM Lung_mTOR ctrl_3",
"Sample ID":"VT_150922_189",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC WT 3_HDM Lung_mTOR ctrl_5",
"Sample ID":"VT_150922_191",
"Factors":{"Genotype":"WT","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 1_HDM Lung_mTOR DCKO_1",
"Sample ID":"VT_150922_193",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 1_HDM Lung_mTOR DCKO_3",
"Sample ID":"VT_150922_195",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 1_HDM Lung_mTOR DCKO_5",
"Sample ID":"VT_150922_197",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 2_HDM Lung_mTOR DCKO_1",
"Sample ID":"VT_150922_199",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 2_HDM Lung_mTOR DCKO_3",
"Sample ID":"VT_150922_201",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 2_HDM Lung_mTOR DCKO_5",
"Sample ID":"VT_150922_203",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 3_HDM Lung_mTOR DCKO_1",
"Sample ID":"VT_150922_205",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 3_HDM Lung_mTOR DCKO_3",
"Sample ID":"VT_150922_207",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
},
{
"Subject ID":"3192015_DC KO 3_HDM Lung_mTOR DCKO_5",
"Sample ID":"VT_150922_209",
"Factors":{"Genotype":"mTOR-APC-KO","HDM_stimulated":"YES"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Lungs and Spleen of WT or mTOR-APC-KO mice were aseptically removed. Spleens were finely chopped with a scalpel in 6-well plates, and digested with 1-1.5mg/mL collagenase type 4 (Worthington Biochemical Corporation) dissolved in HBSS. Digestion was performed for 30 minutes at 37°C, and reactions were stopped with addition of 2mM EDTA. Digestions were passed through 40μm cell strainers to obtain a homogenous cell suspension. To obtain lung suspensions, mice were sacrificed with CO2 and perfused with 5mL PBS injected into the right ventricle. Lungs were dissected into gentleMACS™ C tubes (Miltenyi) and dissociated using a gentleMACS™ octo dissociator using the pre-set program m_lung_01_02. Dissociated lung was digested with 1-1.5mg/mL collagenase type 4 for 30 minutes at 37°C. Lungs were next homogenized with gentleMACS™ octo dissociator program m_lung_02_01, reactions were stopped with 2mM EDTA and digestions passed through 40μm cell strainers. Cells were pelleted (1500-2000rpm/300- 500xg for 5 minutes). Red blood cells were lysed with 1mL Ack lysing buffer (Lonza) for 1 minute and lysis was stopped by addition of ≥ 5 volumes of HBSS. Cells were washed once to obtain single cell suspensions. APCs were enriched with CD11c and CD11b microbeads and MACS manual separation (Miltenyi), according to the manufacturer’s instructions. Enriched cells were stained with live/dead Aqua or Via-Probe™ (BD) and with surface antibody cocktails. Populations were further purified to ≥95% purity with a BD FACSAria cell sorter.","SAMPLE_TYPE":"Sorted cells"},

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

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Acetonitrile (2:1, v/v) was added to cell extracts, wih 3.25ul internal standard. Proteins were removed by centrifugation at 14,000g for 10 min at 4 °C. The supernatant was transferred into autosampler vials for LC-MS analysis.","PROCESSING_METHOD":"precipitation of protein, centrifuge, and remove supernatant","PROCESSING_STORAGE_CONDITIONS":"on ice","EXTRACTION_METHOD":"1:2 sample:acetonitrile","EXTRACT_STORAGE":"supernatant pipette into autosampler vials for mass spectrometer","SAMPLE_SPIKING":"internal standards: [13C6]-D-glucose, [15N]-indole, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Untargeted analysis with HILIC positive mode.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","COLUMN_NAME":"Thermo Accucore HILIC (100 x 2.1mm, 2.6um)","FLOW_GRADIENT":"A: H2O, B: acetonitrile (ACN), C: 2% formic acid in H20. Flow: 0-2min, 10%A-80%B-10%C; 2-7min, 80%A-10%B-10%C; 7-10min, 80%A-10%B-10%C.","FLOW_RATE":".350 ul/min","COLUMN_TEMPERATURE":"30","METHODS_FILENAME":"Metab_HFQE_Setup.docx","INTERNAL_STANDARD":"internal standards: [13C6]-D-glucose, [15N]-indole, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [13C5]-L-glutamic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine","SAMPLE_INJECTION":"10ul","SAMPLING_CONE":"HESI probe with S-lens combination for ESI","ANALYTICAL_TIME":"10min","WEAK_WASH_SOLVENT_NAME":"water with 10% methanol"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Clinical Biomarkers Laboratory","OPERATOR_NAME":"ViLinh Tran","DETECTOR_TYPE":"orbitrap","SOFTWARE_VERSION":"Thermo Excalibur 2.2","ACQUISITION_DATE":"9/23/2015-9/25/2015","DATA_FORMAT":".raw, .cdf"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_TEMPERATURE":"300C","CAPILLARY_VOLTAGE":"44V","IONIZATION":"electrospray ionization","MASS_ACCURACY":"10ppm","SPRAY_VOLTAGE":"3.5 kV","MS_RESULTS_FILE":"ST000657_AN001003_Results.txt UNITS:au"}

}