{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003245","ANALYSIS_ID":"AN005315","PROJECT_ID":"PR002015","VERSION":"1","CREATED_ON":"May 27, 2024, 9:55 am"},
"PROJECT":{"PROJECT_TITLE":"Zeb1-mediated control of the phospholipid PUFA/MUFA ratio in EMT/plasticity-associated 1 cancer cell ferroptosis","PROJECT_SUMMARY":"Therapy resistance and metastasis, the most fatal steps in cancer, are often triggered by a (partial) activation of the epithelial-mesenchymal-transition (EMT)-program. A mesenchymal phenotype predisposes to ferroptosis, a cell death pathway exerted by an iron and oxygen-radical mediated peroxidation of phospholipids containing polyunsaturated fatty acids (PUFAs). We here describe that various forms of EMT-activation increase ferroptosis-susceptibility in cancer cells, which depends on the EMT-transcription factor Zeb1. To further investigate the underlying mechanisms of an EMT/Zeb1-coupled ferroptosis sensitivity, we analyzed key determinants of ferroptotic cell death, focusing on the proportion and (per)oxidation of fatty acid species in phospholipid subclasses. Using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), we demonstrate that GPX4 inhibition in human breast cancer MDA-MB-231 cells (Zeb1high) led to a rapid (per)oxidation of PUFA-containing phospholipids (oxPL), which is absent in cells depleted of Zeb1 (shZeb1). Mechanistically, Zeb1 increases the ratio of phospholipids containing pro-ferroptotic PUFAs over cyto-protective monounsaturated fatty acids (MUFAs) in MDA-MB-231 cells, tumor-derived pancreatic cancer KPC cells as well as mice tumor allografts via the modulation of crucial lipogenic enzymes.","INSTITUTE":"University of Innsbruck","DEPARTMENT":"Michael Popp Institute","LAST_NAME":"Koeberle","FIRST_NAME":"Andreas","ADDRESS":"Mitterweg 24, Innsbruck, Tyrol, 6020, Austria","EMAIL":"Andreas.Koeberle@uibk.ac.at","PHONE":"+43 512 507 57903","FUNDING_SOURCE":"the Austrian Science Fund (FWF) (P 36299), the German Research Council (GRK 1715), and the Phospholipid Research Center (Grant Number AKO‐2019‐070/2‐1, AKO-2O22-100/2-2), the Tyrolean Science Fund (TWF) (F.33467/7-2021).","PUBLICATIONS":"in revision","CONTRIBUTORS":"Zhigang Rao, Jie Zhang, André Gollowitzer, Leonhard Bereuter, Andreas Koeberle"},
"STUDY":{"STUDY_TITLE":"Exploration of Zeb1-dependent changes in the lipidome of MDA-MB-231 cells","STUDY_SUMMARY":"Human breast cancer MDA-MB-231 wildtype (WT) cells and the stably transduced MDA-MB-231 shZeb1 (stable Zeb1 knockdown) and shCtrl cell lines (control cell line for the stable Zeb1 knockdown) (Spaderna et al. 2008, DOI: 10.1158/0008-5472.CAN-07-5682) were analyzed for their phospholipid profile by UPLC-MS/MS.","INSTITUTE":"University of Innsbruck","DEPARTMENT":"Michael Popp Institute","LAST_NAME":"Koeberle","FIRST_NAME":"Andreas","ADDRESS":"Mitterweg 24, Innsbruck, Tyrol, 6020, Austria","EMAIL":"Andreas.Koeberle@uibk.ac.at","PHONE":"+43 512 507 57903"},
"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__MDA_MB_231_WT_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n1_2h_WT_DMSO_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n2_2h_WT_DMSO_10",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n3_2h_WT_DMSO_19",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Wild-type"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#1_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shGFP_#4_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n1_2h_sh-Ctrl_DMSO_4",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n2_2h_sh-Ctrl_DMSO_13",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n3_2h_sh-Ctrl_DMSO_22",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#13_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics__shZEB1#F10_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PE","RAW_FILE_NAME(Raw file name for PC)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PC","RAW_FILE_NAME(Raw file name for PI)":"190905_AG_Brabletz_ZEB1_EMT_Lipidomics_PI"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n1_2h_sh-ZEB1_DMSO_7",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n2_2h_sh-ZEB1_DMSO_16",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"210514_MDA_ZEB1_n3_2h_sh-ZEB1_DMSO_25",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"210514_MDA_ZEB1_PE_dil_1_10_std_1ul_JZ_PE_MRM_002","RAW_FILE_NAME(Raw file name for PC)":"210514_MDA_ZEB1_PC_dil_1_10_std_1ul_JZ_PC_MRM_002","RAW_FILE_NAME(Raw file name for PI)":"210514_MDA_ZEB1_PI_dil_1_10_std_1ul_JZ_PI_MRM_002"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PE_5",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PE_6",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PE_7",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PE_8",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PE_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PE_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PE_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PE_4",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"220408_MDA shCtrl shZEB1_PE","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PC_5",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PC_6",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PC_7",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shCtrl_1_10_PC_8",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PC_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PC_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PC_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"220408_MDA shZEB1_1_10_PC_4",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"220408_MDA shZEB1 shCtrl_PC","RAW_FILE_NAME(Raw file name for PI)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shCTRL_5",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shCTRL_6",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shCTRL_7",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shCTRL_8",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"control for Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shZEB1_1",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shZEB1_2",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shZEB1_3",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
},
{
"Subject ID":"-",
"Sample ID":"230309_shCTRL shZEB1_Rao_shZEB1_4",
"Factors":{"Sample source":"MDA-MB-231 cells","Genotype":"Zeb1 stable knockdown"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name for PE)":"-","RAW_FILE_NAME(Raw file name for PC)":"-","RAW_FILE_NAME(Raw file name for PI)":"230309_shCTRL shZEB1_Rao_1-10 dilu_PI"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cultured cells were washed, trypsinized, counted and flash-frozen in liquid N2 and stored at -80°C.","SAMPLE_TYPE":"BCa cells","STORAGE_CONDITIONS":"-80℃"},
"TREATMENT":{"TREATMENT_SUMMARY":"Human breast cancer MDA-MB-231 wildtype (WT) cells and the stably transduced MDA-MB-231 shZeb1 (stable Zeb1 knockdown) and shCtrl cell lines (control cell line for the stable Zeb1 knockdown) (Spaderna et al. 2008, DOI: 10.1158/0008-5472.CAN-07-5682) were collected, snap-frozen and stored at -80°C."},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Phospholipids were extracted from cell pellets by successive addition of PBS pH 7.4, methanol, chloroform, and saline to a final ratio of 14:34:35:17. Evaporation of the organic layer yielded a lipid film that was dissolved in methanol and subjected to UPLC-MS/MS.","EXTRACT_STORAGE":"-80℃"},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Chromatographic separation of phospholipids was carried out on an Acquity BEH C8 column (1.7 μm, 2.1×100 mm, Waters, Milford, MA) using an Acquity UHPLC.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity H-Class","COLUMN_NAME":"Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)","SOLVENT_A":"water/acetonitrile 90/10, 2 mM ammonium acetate","SOLVENT_B":"water/acetonitrile 5/95, 2 mM ammonium acetate","FLOW_GRADIENT":"The gradient was ramped from 75 to 85% B over 5 min and further increased to 100% B within 2 min, followed by isocratic elution for another 2 min","FLOW_RATE":"0.75 ml/min","COLUMN_TEMPERATURE":"45"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500+","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Targeted MRM with pre-optimized settings and subsequent automated integration of selected signals using Analyst 1.6.3 or Analyst 1.7.1 (Sciex)."},
"MS_METABOLITE_DATA":{
"Units":"relative intensities",
"Data":[{"Metabolite":"PE 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