{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001707","ANALYSIS_ID":"AN002781","VERSION":"1","CREATED_ON":"February 22, 2021, 2:18 pm"},

"PROJECT":{"PROJECT_TITLE":"Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations","PROJECT_SUMMARY":"Inactivating mutations including both germline and somatic mutations in the adenomatous polyposis coli (APC) gene drives most familial and sporadic colorectal cancers. Understanding the metabolic implications of this mutation will aid to establish its wider impact on cellular behaviour and potentially inform clinical decisions. However, to date, alterations in lipid metabolism induced by APC mutations remain unclear. Intestinal organoids have gained widespread popularity in studying colorectal cancer and chemotherapies, because their three-dimensional structure more accurately mimics an in vivo environment. Here, we aimed to investigate intra-cellular lipid disturbances induced by APC gene mutations in intestinal organoids using a reversed-phase ultra-high-performance liquid chromatography mass spectrometry (RP-UHPLC-MS)-based lipid profiling method. Lipids of the organoids grown from either wildtype (WT) or mice with Apc mutations (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) were extracted and analysed using RP-UHPLC-MS. Concentrations of phospholipids (e.g. PC(16:0/16:0), PC(18:1/20:0), PC(38:0), PC(18:1/22:1)), ceramides (e.g. Cer(d18:0/22:0), Cer(d42:0), Cer(d18:1/24:1)) and hexosylceramide (e.g. HexCer(d18:1/16:0), HexCer(d18:1/22:0)) were higher in Apcfl/fl organoids, whereas levels of sphingomyelins (e.g. SM(d18:1/14:0), SM(d18:1/16:0) ) were lower compared to WT. These observations indicate that cellular metabolism of sphingomyelin was upregulated, resulting in the cellular accumulation of ceramides and production of HexCer due to the absence of Apcfl/fl in the organoids. Our observations demonstrated lipid profiling of organoids and provided an enhanced insight into the effects of the APC mutations on lipid metabolism, making for a valuable addition to screening options of the organoid lipidome.","INSTITUTE":"Imperial College London","LAST_NAME":"Li","FIRST_NAME":"Jia","ADDRESS":"Imperial College London Road, South Kensington, London, London, SW7 2AZ, United Kingdom","EMAIL":"jia.li@imperial.ac.uk","PHONE":"02075943230"},

"STUDY":{"STUDY_TITLE":"Lipid Profiling of Mouse Intestinal Organoids for studying APC Mutations","STUDY_SUMMARY":"Inactivating mutations including both germline and somatic mutations in the adenomatous polyposis coli (APC) gene drives most familial and sporadic colorectal cancers. Understanding the metabolic implications of this mutation will aid to establish its wider impact on cellular behaviour and potentially inform clinical decisions. However, to date, alterations in lipid metabolism induced by APC mutations remain unclear. Intestinal organoids have gained widespread popularity in studying colorectal cancer and chemotherapies, because their three-dimensional structure more accurately mimics an in vivo environment. Here, we aimed to investigate intra-cellular lipid disturbances induced by APC gene mutations in intestinal organoids using a reversed-phase ultra-high-performance liquid chromatography mass spectrometry (RP-UHPLC-MS)-based lipid profiling method. Lipids of the organoids grown from either wildtype (WT) or mice with Apc mutations (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) were extracted and analysed using RP-UHPLC-MS. Concentrations of phospholipids (e.g. PC(16:0/16:0), PC(18:1/20:0), PC(38:0), PC(18:1/22:1)), ceramides (e.g. Cer(d18:0/22:0), Cer(d42:0), Cer(d18:1/24:1)) and hexosylceramide (e.g. HexCer(d18:1/16:0), HexCer(d18:1/22:0)) were higher in Apcfl/fl organoids, whereas levels of sphingomyelins (e.g. SM(d18:1/14:0), SM(d18:1/16:0) ) were lower compared to WT. These observations indicate that cellular metabolism of sphingomyelin was upregulated, resulting in the cellular accumulation of ceramides and production of HexCer due to the absence of Apcfl/fl in the organoids. Our observations demonstrated lipid profiling of organoids and provided an enhanced insight into the effects of the APC mutations on lipid metabolism, making for a valuable addition to screening options of the organoid lipidome.","INSTITUTE":"Imperial College London","LAST_NAME":"Li","FIRST_NAME":"Jia","ADDRESS":"Imperial College London, UK","EMAIL":"jia.li@imperial.ac.uk","PHONE":"00442075943230"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_1",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_1","sample replicate IDs":"1","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_2",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_2","sample replicate IDs":"2","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_3",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_3","sample replicate IDs":"3","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_4",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_4","sample replicate IDs":"4","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_5",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_5","sample replicate IDs":"5","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_6",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_6","sample replicate IDs":"6","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_7",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_7","sample replicate IDs":"7","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"NEG_WT_m1641_8",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1641_8","sample replicate IDs":"8","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_1",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_1","sample replicate IDs":"1","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_2",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_2","sample replicate IDs":"2","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_3",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_3","sample replicate IDs":"3","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_4",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_4","sample replicate IDs":"4","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_5",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_5","sample replicate IDs":"5","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_6",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_6","sample replicate IDs":"6","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_7",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_7","sample replicate IDs":"7","MS mode":"negative"}
},
{
"Subject ID":"m1663",
"Sample ID":"NEG_WT_m1663_8",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_WT_m1663_8","sample replicate IDs":"8","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_1",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_1","sample replicate IDs":"1","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_2",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_2","sample replicate IDs":"2","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_3",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_3","sample replicate IDs":"3","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_4",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_4","sample replicate IDs":"4","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_5",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_5","sample replicate IDs":"5","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_6",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_6","sample replicate IDs":"6","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_7",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_7","sample replicate IDs":"7","MS mode":"negative"}
},
{
"Subject ID":"m830",
"Sample ID":"NEG_APC_m830_8",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m830_8","sample replicate IDs":"8","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_1",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_1","sample replicate IDs":"1","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_2",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_2","sample replicate IDs":"2","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_3",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_3","sample replicate IDs":"3","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_4",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_4","sample replicate IDs":"4","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_5",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_5","sample replicate IDs":"5","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_6",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_6","sample replicate IDs":"6","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_7",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_7","sample replicate IDs":"7","MS mode":"negative"}
},
{
"Subject ID":"m862",
"Sample ID":"NEG_APC_m862_8",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_APC_m862_8","sample replicate IDs":"8","MS mode":"negative"}
},
{
"Subject ID":"quality control",
"Sample ID":"NEG_QC1",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_QC1","sample replicate IDs":"quality control","MS mode":"negative"}
},
{
"Subject ID":"quality control",
"Sample ID":"NEG_QC2",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_QC2","sample replicate IDs":"quality control","MS mode":"negative"}
},
{
"Subject ID":"quality control",
"Sample ID":"NEG_QC3",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_QC3","sample replicate IDs":"quality control","MS mode":"negative"}
},
{
"Subject ID":"quality control",
"Sample ID":"NEG_QC4",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_QC4","sample replicate IDs":"quality control","MS mode":"negative"}
},
{
"Subject ID":"quality control",
"Sample ID":"NEG_QC5",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_QC5","sample replicate IDs":"quality control","MS mode":"negative"}
},
{
"Subject ID":"blank",
"Sample ID":"NEG_Blank",
"Factors":{"Genotype":"blank"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Blank","sample replicate IDs":"blank","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_2_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_2_1","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_2_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_2_2","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_2_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_2_3","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_4_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_4_1","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_4_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_4_2","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_4_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_4_3","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_8_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_8_1","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_8_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_8_2","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"NEG_Dilution1_8_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"NEG_Dilution1_8_3","sample replicate IDs":"quality control dilutions","MS mode":"negative"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_1",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_1","sample replicate IDs":"1","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_2",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_2","sample replicate IDs":"2","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_3",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_3","sample replicate IDs":"3","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_4",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_4","sample replicate IDs":"4","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_5",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_5","sample replicate IDs":"5","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_6",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_6","sample replicate IDs":"6","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_7",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_7","sample replicate IDs":"7","MS mode":"positive"}
},
{
"Subject ID":"m1641",
"Sample ID":"POS_WT_m1641_8",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1641_8","sample replicate IDs":"8","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_1",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_1","sample replicate IDs":"1","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_2",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_2","sample replicate IDs":"2","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_3",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_3","sample replicate IDs":"3","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_4",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_4","sample replicate IDs":"4","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_5",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_5","sample replicate IDs":"5","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_6",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_6","sample replicate IDs":"6","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_7",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_7","sample replicate IDs":"7","MS mode":"positive"}
},
{
"Subject ID":"m1663",
"Sample ID":"POS_WT_m1663_8",
"Factors":{"Genotype":"wildtype"},
"Additional sample data":{"RAW_FILE_NAME":"POS_WT_m1663_8","sample replicate IDs":"8","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_1",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_1","sample replicate IDs":"1","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_2",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_2","sample replicate IDs":"2","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_3",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_3","sample replicate IDs":"3","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_4",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_4","sample replicate IDs":"4","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_5",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_5","sample replicate IDs":"5","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_6",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_6","sample replicate IDs":"6","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_7",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_7","sample replicate IDs":"7","MS mode":"positive"}
},
{
"Subject ID":"m830",
"Sample ID":"POS_APC_m830_8",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m830_8","sample replicate IDs":"8","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_1",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_1","sample replicate IDs":"1","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_2",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_2","sample replicate IDs":"2","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_3",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_3","sample replicate IDs":"3","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_4",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_4","sample replicate IDs":"4","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_5",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_5","sample replicate IDs":"5","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_6",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_6","sample replicate IDs":"6","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_7",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_7","sample replicate IDs":"7","MS mode":"positive"}
},
{
"Subject ID":"m862",
"Sample ID":"POS_APC_m862_8",
"Factors":{"Genotype":"APC"},
"Additional sample data":{"RAW_FILE_NAME":"POS_APC_m862_8","sample replicate IDs":"8","MS mode":"positive"}
},
{
"Subject ID":"quality control",
"Sample ID":"POS_QC1",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"POS_QC1","sample replicate IDs":"quality control","MS mode":"positive"}
},
{
"Subject ID":"quality control",
"Sample ID":"POS_QC2",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"POS_QC2","sample replicate IDs":"quality control","MS mode":"positive"}
},
{
"Subject ID":"quality control",
"Sample ID":"POS_QC3",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"POS_QC3","sample replicate IDs":"quality control","MS mode":"positive"}
},
{
"Subject ID":"quality control",
"Sample ID":"POS_QC4",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"POS_QC4","sample replicate IDs":"quality control","MS mode":"positive"}
},
{
"Subject ID":"quality control",
"Sample ID":"POS_QC5",
"Factors":{"Genotype":"quality control"},
"Additional sample data":{"RAW_FILE_NAME":"POS_QC5","sample replicate IDs":"quality control","MS mode":"positive"}
},
{
"Subject ID":"blank",
"Sample ID":"POS_Blank",
"Factors":{"Genotype":"blank"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Blank","sample replicate IDs":"blank","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_2_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_2_1","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_2_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_2_2","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_2_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_2_3","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_4_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_4_1","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_4_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_4_2","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_4_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_4_3","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_8_1",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_8_1","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_8_2",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_8_2","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
},
{
"Subject ID":"quality control dilutions",
"Sample ID":"POS_Dilution1_8_3",
"Factors":{"Genotype":"quality control dilutions"},
"Additional sample data":{"RAW_FILE_NAME":"POS_Dilution1_8_3","sample replicate IDs":"quality control dilutions","MS mode":"positive"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Control (Lgr5–EGFP-IRES-CreERT2 Apc+/+) or experimental (Lgr5–EGFP-IRES-CreERT2 Apcfl/fl) adult mice were administered tamoxifen (80 mg/kg) daily via intraperitoneal injection for 4 consecutive days to induce Cre expression. Fourteen days following induction mice were sacrificed (cervical dislocation) and their intestinal cells were harvested for organoid culture of WT or Apc deficient intestinal stem cells.","SAMPLE_TYPE":"Intestine"},

"TREATMENT":{"TREATMENT_SUMMARY":"no treatment was applied"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Following aqueous extraction using cold methanol and water (v:v, 1:1), 1 ml of pre-chilled dichloromethane (DCM)/methanol (v:v, 3:1) was added to the organoid samples. Samples were bead-beaten for 40 seconds followed by five minutes of chilling on dry ice. This procedure was repeated three times before being centrifuged for 10 mins at 21,000 rcf at 4ºC. A total of 600 μl of supernatant from each sample was transferred to a glass vial. Another 200 μl of supernatant from each sample was pooled into a 15-ml Falcon tube to form a quantity control (QC) sample and split into several aliquots of 600 μl each. An extraction blank sample was included to control for any potential contaminant introduced throughout the extraction process. Samples were dried by evaporation over night at room temperature and stored at -40˚C until further analysis. The dried extracts were reconstituted in 100 μl of water/acetonitrile (ACN)/isopropanol (IPA), (v:v:v, 1:1:3,). The lipids were dissolved by vigorous vortexing for five minutes, followed by five minutes of sonication. This step was repeated three times to allow the dry extracts to thoroughly dissolve in the solvent. Samples were subsequently centrifuged at 21,000 rcf for 10 minutes at 4ºC and transferred to 150-μl glass inserts placed in glass vials (Waters)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Acquity UPLC","COLUMN_NAME":"Waters Acquity C18 CSH (2.1 x 10 mm, 1.7 μm)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"jli_20210217_034113_PR_MS_Methodology.docx"},

"MS":{"INSTRUMENT_NAME":"Waters Synapt G2 S QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"refer to Methodology.docx","MS_RESULTS_FILE":"ST001707_AN002781_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Seconds"}

}