{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001290","ANALYSIS_ID":"AN002144","VERSION":"1","CREATED_ON":"December 17, 2019, 1:42 pm"},

"PROJECT":{"PROJECT_TITLE":"Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma.","PROJECT_TYPE":"Untargeted metabolomics","PROJECT_SUMMARY":"Medulloblastoma (MB), the most common malignant pediatric brain tumor, has high propensity to metastasize. Currently, the standard treatment for MB patients includes radiation therapy administered to the entire brain and spine for the purpose of treating or preventing against metastasis. Due to this aggressive treatment, the majority of long-term survivors will be left with permanent and debilitating neurocognitive impairments and, for the 30-40% patients that fail to respond to radiation, all will relapse with terminal metastatic disease. An understanding of the underlying biology that drives MB metastasis is lacking, and is critically needed in order to develop targeted therapeutics for its prevention. To examine the metastatic biology of sonic hedgehog (SHH) MB, the human MB subgroup with the worst clinical outcome, we first generated a robust SmoA1-Math-GFP mouse model that reliably reproduces human SHH MB whereby metastases can be visualized under fluorescence microscopy. Lipidome alterations associated with metastasis were then investigated by applying Ultra-Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) under both positive and negative ionization modes to primary tumor samples collected from mice with (n=18) and without (n=7) metastasis. This study provides the first insights into dysregulations of lipid metabolism associated with SHH MB metastatic progression, and thus serves as a guide toward novel targeted therapies.","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"Chemistry","LABORATORY":"Fernández","LAST_NAME":"Huang","FIRST_NAME":"Danning","ADDRESS":"901 Atlantic Dr NE, Atlanta, GA, 30332, USA","EMAIL":"dhuang74@gatech.edu","PHONE":"404-512-7523"},

"STUDY":{"STUDY_TITLE":"Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma.","STUDY_TYPE":"Untargeted metabolomics","STUDY_SUMMARY":"Metabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to mice brain tissue samples collected from SmoA1-Math-GFP mice with (n=18) and without (n=7) metastasis. All samples were analyzed using reverse phase (RP) UPLC-MS analysis in positive and negative ion modes.","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"Chemistry","LABORATORY":"Fernández","LAST_NAME":"Huang","FIRST_NAME":"Danning","ADDRESS":"901 Atlantic Dr NE","EMAIL":"dhuang74@gatech.edu","PHONE":"4045127523","NUM_GROUPS":"2","TOTAL_SUBJECTS":"25","NUM_MALES":"5","NUM_FEMALES":"20"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"SmoA1-Math-GFP","AGE_OR_AGE_RANGE":"12-36 weeks","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SG215",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/20/14","Sex":"F","Age (weeks)":"26","RAW_FILE_NAME":"SG215.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG218",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/20/14","Sex":"F","Age (weeks)":"26","RAW_FILE_NAME":"SG218.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG174",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"5/13/14","Sex":"M","Age (weeks)":"30","RAW_FILE_NAME":"SG174.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG221",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/21/14","Sex":"F","Age (weeks)":"13","RAW_FILE_NAME":"SG221.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG223",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/21/14","Sex":"F","Age (weeks)":"14","RAW_FILE_NAME":"SG223.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG203",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"6/15/14","Sex":"F","Age (weeks)":"22","RAW_FILE_NAME":"SG203.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG175",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"3/12/14","Sex":"F","Age (weeks)":"36","RAW_FILE_NAME":"SG175.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG204",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"6/15/14","Sex":"F","Age (weeks)":"23","RAW_FILE_NAME":"SG204.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG217",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/21/14","Sex":"F","Age (weeks)":"20","RAW_FILE_NAME":"SG217.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA11",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"7/10/14","Sex":"F","Age (weeks)":"22","RAW_FILE_NAME":"SGTA11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA9",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"4/28/14","Sex":"F","Age (weeks)":"27","RAW_FILE_NAME":"SGTA9.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA10",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"6/10/14","Sex":"F","Age (weeks)":"21","RAW_FILE_NAME":"SGTA10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA4",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"2/1/14","Sex":"F","Age (weeks)":"18","RAW_FILE_NAME":"SGTA4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA3",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"10/16/13","Sex":"F","Age (weeks)":"34","RAW_FILE_NAME":"SGTA3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG105",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"9/23/14","Sex":"M","Age (weeks)":"29","RAW_FILE_NAME":"SG105.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG138",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"11/2/13","Sex":"F","Age (weeks)":"21","RAW_FILE_NAME":"SG138.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG113",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"9/10/13","Sex":"M","Age (weeks)":"34","RAW_FILE_NAME":"SG113.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CASE40",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PT"},
"Additional sample data":{"DOB":"11/20/14","Sex":"F","Age (weeks)":"18","RAW_FILE_NAME":"CASE40.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA13",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"4/28/14","Sex":"F","Age (weeks)":"34","RAW_FILE_NAME":"SGTA13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG228",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"7/20/14","Sex":"M","Age (weeks)":"26","RAW_FILE_NAME":"SG228.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA12",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"6/10/14","Sex":"F","Age (weeks)":"26","RAW_FILE_NAME":"SGTA12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SGTA",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"10/16/13","Sex":"F","Age (weeks)":"29","RAW_FILE_NAME":"SGTA.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG191",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"5/13/14","Sex":"F","Age (weeks)":"13","RAW_FILE_NAME":"SG191.raw"}
},
{
"Subject ID":"-",
"Sample ID":"CASE41",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"8/18/14","Sex":"M","Age (weeks)":"32","RAW_FILE_NAME":"CASE41.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SG222",
"Factors":{"Mice strain":"SmoA1-Math-GFP","Group":"PTMT"},
"Additional sample data":{"DOB":"7/20/14","Sex":"F","Age (weeks)":"12","RAW_FILE_NAME":"SG222.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice brain and spinal cord were dissected from each mouse and fluorescence microscopy was used to visualize the tumors. Mice having a GFP signal in the cerebellum only were designated as having a primary tumor without metastasis (PT group, n=18). Mice having a strong GFP signal in the cerebellum and positive GFP signal in the spinal cord were designated as having a primary tumor with metastasis (PTMT group, n=7). With aid of GFP visualization, the primary tumor in each mouse brain was cut from the cerebellum, and immediately frozen using liquid nitrogen, and stored at -80 °C.","SAMPLE_TYPE":"Brain","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"SmoA1-Math1-GFP mice were generated by crossing SmoA1 mice with Math1-driven GFP reporter mice. All mice were kept under the same condition and typically developed detectable MB tumors by MR imaging and clinical symptoms around 23 weeks."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen mice brain tissue samples were cryo-pulverized with liquid nitrogen and weighed. 2-propanol (20 uL/mg) was added to the cryo-pulverized tissue samples to precipitate proteins. Samples were vortex-mixed for 1 min, and centrifuged at 13,000 rpm for 7 min. Following centrifugation, 100 uL of supernatant was transferred to an autosampler vial and analyzed with UPLC-MS. A blank sample, prepared with 100 uL 2-propanol, underwent the same process as the murine tumor samples. A pooled quality control (QC) sample was prepared by mixing a 10 uL aliquot of supernatant of each sample."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters Acquity BEH C18 (50 x 2.1mm, 1.7 um)","COLUMN_TEMPERATURE":"55","SOLVENT_A":"water/acetonitrile (40:60 v/v), 10 mM ammonium formate and 0.1% formic acid","SOLVENT_B":"acetonitrile/isopropanol (10:90 v/v), 10 mM ammonium formate and 0.1% formic acid","SAMPLE_INJECTION":"5μL"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Samples were analyzed in positive and negative ion modes for RP chromatography. Spectral features were extracted from the raw data using Progenesis QI v2.1 software.","CAPILLARY_TEMPERATURE":"275 °C","SPRAY_VOLTAGE":"-2.8 kV","MS_RESULTS_FILE":"ST001290_AN002144_Results.txt UNITS:Normalized Peak Abundance Has m/z:Yes Has RT:Yes RT units:Minutes"}

}