{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001745","ANALYSIS_ID":"AN002840","VERSION":"1","CREATED_ON":"April 19, 2021, 4:18 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic profiling of the rat hippocampus across developmental ages and after learning.","PROJECT_TYPE":"Neuroscience","PROJECT_SUMMARY":"The metabolic mechanisms underlying the formation of early-life episodic memories remain poorly characterized. To fill this knowledge gap, we employed an untargeted metabolomic analysis in rats to determine how the hippocampal metabolome changes over the course of post-natal development under basal conditions and following inhibitory avoidance (IA) training, an aversive episodic event. We found that unique metabolomic profiles accompany learning at different ages. Subsequent biochemical and behavioral studies based on unique metabolomic regulations in the infant hippocampus established that infantile learning selectively recruits the glutathione-mediated antioxidant defenses for the formation of infantile memory.","INSTITUTE":"New York University","DEPARTMENT":"Center for Neural Science (NYU)","LABORATORY":"Cristina Alberini","LAST_NAME":"Bessieres","FIRST_NAME":"Benjamin","ADDRESS":"4 Washington Place, Room 623","EMAIL":"bjb11@nyu.edu","PHONE":"6315684274","FUNDING_SOURCE":"NIH"},

"STUDY":{"STUDY_TITLE":"Metabolomic profiling of the rat hippocampus across developmental ages and after learning","STUDY_TYPE":"Developmental study","STUDY_SUMMARY":"Little is known about how the hippocampal metabolomic profile changes across development and in response to learning at different ages. To fill this knowledge gap, we employed an untargeted metabolomic analyses in rats to determine how the hippocampal metabolome changes over the course of post-natal development under basal conditions and following inhibitory avoidance (IA) training, an aversive episodic event. We found that unique metabolomic profiles accompany learning at different ages. Subsequent biochemical and behavioral studies based on unique metabolomic regulations in the infant hippocampus established that infantile learning selectively recruits the glutathione-mediated antioxidant defenses for the formation of infantile memory.","INSTITUTE":"New York University","DEPARTMENT":"Center for Neural Science (NYU)","LABORATORY":"Cristina Alberini","LAST_NAME":"Bessieres","FIRST_NAME":"Benjamin","ADDRESS":"4 Washington Place, Room 623","EMAIL":"bjb11@nyu.edu","PHONE":"6315684274","NUM_GROUPS":"8","TOTAL_SUBJECTS":"52","NUM_MALES":"35","NUM_FEMALES":"17"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Rattus norvegicus","TAXONOMY_ID":"10116","GENOTYPE_STRAIN":"Long Evans","AGE_OR_AGE_RANGE":"From post-natal day 1 (PN1) to PN80","WEIGHT_OR_WEIGHT_RANGE":"5g-250g","GENDER":"Male and female","ANIMAL_ANIMAL_SUPPLIER":"Envigo","ANIMAL_HOUSING":"Animal facility at NYU","ANIMAL_LIGHT_CYCLE":"7am-7pm"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"HD4_PN1_1",
"Sample ID":"NYSM-00454",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN1_2",
"Sample ID":"NYSM-00455",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN1_3",
"Sample ID":"NYSM-00456",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN1_4",
"Sample ID":"NYSM-00457",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN1_5",
"Sample ID":"NYSM-00458",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN7_1",
"Sample ID":"NYSM-00459",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN7_2",
"Sample ID":"NYSM-00460",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN7_3",
"Sample ID":"NYSM-00461",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN7_4",
"Sample ID":"NYSM-00462",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN7_5",
"Sample ID":"NYSM-00463",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_1",
"Sample ID":"NYSM-00464",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_2",
"Sample ID":"NYSM-00465",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_3",
"Sample ID":"NYSM-00466",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_4",
"Sample ID":"NYSM-00467",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_5",
"Sample ID":"NYSM-00468",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_6",
"Sample ID":"NYSM-00469",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_7",
"Sample ID":"NYSM-00470",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_8",
"Sample ID":"NYSM-00471",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_9",
"Sample ID":"NYSM-00472",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_10",
"Sample ID":"NYSM-00473",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_11",
"Sample ID":"NYSM-00474",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_12",
"Sample ID":"NYSM-00475",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_13",
"Sample ID":"NYSM-00476",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN17_14",
"Sample ID":"NYSM-00477",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_1",
"Sample ID":"NYSM-00478",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_2",
"Sample ID":"NYSM-00479",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_3",
"Sample ID":"NYSM-00480",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_4",
"Sample ID":"NYSM-00481",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_5",
"Sample ID":"NYSM-00482",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_6",
"Sample ID":"NYSM-00483",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_7",
"Sample ID":"NYSM-00484",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_8",
"Sample ID":"NYSM-00485",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_9",
"Sample ID":"NYSM-00486",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_10",
"Sample ID":"NYSM-00487",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_11",
"Sample ID":"NYSM-00488",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_12",
"Sample ID":"NYSM-00489",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_13",
"Sample ID":"NYSM-00490",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN24_14",
"Sample ID":"NYSM-00491",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"F","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_1",
"Sample ID":"NYSM-00492",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_2",
"Sample ID":"NYSM-00493",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_3",
"Sample ID":"NYSM-00494",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_4",
"Sample ID":"NYSM-00495",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_5",
"Sample ID":"NYSM-00496",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_6",
"Sample ID":"NYSM-00497",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_7",
"Sample ID":"NYSM-00498",
"Factors":{"Treatment":"naive"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_8",
"Sample ID":"NYSM-00499",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_9",
"Sample ID":"NYSM-00500",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_10",
"Sample ID":"NYSM-00501",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_11",
"Sample ID":"NYSM-00502",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_12",
"Sample ID":"NYSM-00503",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_13",
"Sample ID":"NYSM-00504",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
},
{
"Subject ID":"HD4_PN80_14",
"Sample ID":"NYSM-00505",
"Factors":{"Treatment":"trained"},
"Additional sample data":{"Sex":"M","RAW_FILE_NAME":"MyData"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Rats trained in inhibitory avoidance at PN17, PN24, and PN80, and the untrained (naive) control rats were euthanized by decapitation (1 hour after IA training). Their brains were quickly removed and placed in ice-cold phosphate-buffered saline (1X). Whole hippocampal samples were dissected and immediately snap-frozen in isopentane on dry ice. All samples were stored at -80°C until processing. Frozen samples were shipped in dry ice to Metabolon Inc. (Morrisville, NC, USA) for metabolomic analysis using a proprietary methodology. Extraction of samples was performed using a MicroLab STAR automated liquid handling robot (Hamilton Robotics, Inc., Reno, NV, USA); 450 μL of methanol was added to 100 μo of sample to precipitate proteins. Four recovery standards (DL-2-fluorophenylglycine, tridecanoic acid, cholesterol-d6 and 4-chlorophenylalanine) were added to each sample to determine extraction efficiency. To remove proteins, dissociate small molecules bound to protein, and recover metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation (1300 g for 10 min at room temperature). The resultant supernatants were placed in a TurboVap (Zymark) to remove the organic solvent. Each sample extract was then divided into five equal aliquots, dried under nitrogen, and stored in vacuo prior to metabolomic profiling.","SAMPLE_TYPE":"Brain","COLLECTION_METHOD":"Brain dissection","COLLECTION_LOCATION":"New York University","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Metabolomic profiling was carried out on hippocampal extracts (five to seven individual replicates) obtained from untrained rats at four early, prepuberal developmental ages [postnatal day 1 (PN1), PN7, PN17 and PN24] and compared to the profile obtained from young adults (PN80). Additionally, the metabolomic profiles of the hippocampus 1 hour after IA training at PN17, PN24, and PN80 were compared with those of age-matched untrained (naive) control rats."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction of samples was performed using a MicroLab STAR automated liquid handling robot (Hamilton Robotics, Inc., Reno, NV, USA); 450 μL of methanol was added to 100 μL of sample to precipitate proteins. Four recovery standards (DL-2-fluorophenylglycine, tridecanoic acid, cholesterol-d6 and 4-chlorophenylalanine) were added to each sample to determine extraction efficiency. To remove proteins, dissociate small molecules bound to protein, and recover metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation (1300 g for 10 min at room temperature). The resultant supernatants were placed in a TurboVap (Zymark) to remove the organic solvent. Each sample extract was then divided into five equal aliquots, dried under nitrogen, and stored in vacuo prior to metabolomic profiling."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The first two aliquots were analyzed by two separate reverse-phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI): one aliquot was analyzed using acidic positive-ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient-eluted from a C18 column (2 mm × 100 mm Waters UPLC BEH C18 1.7 µm column held at 40°C) using 5% water and 95% methanol and containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA) at pH 3.5. The second aliquot was also analyzed using acidic positive-ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient-eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA at pH 3.5. A third aliquot was analyzed by RP/UPLC-MS/MS using basic negative-ion mode ESI in a separate dedicated C18 column. The basic extracts were gradient-eluted from the column using methanol (95%) and water (5%) with 6.5 mM ammonium bicarbonate at pH 8.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (100 x 2mm, 1.7um)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"A third aliquot was analyzed by RP/UPLC-MS/MS using basic negative-ion mode ESI in a separate dedicated C18 column. The basic extracts were gradient-eluted from the column using methanol (95%) and water (5%) with 6.5 mM ammonium bicarbonate at pH 8."},

"MS_METABOLITE_DATA":{
"Units":"pmoles/l",

"Data":[{"Metabolite":"1,5-anhydroglucitol (1,5-AG)","NYSM-00454":"830482","NYSM-00455":"1111889","NYSM-00456":"796184","NYSM-00457":"1527624","NYSM-00458":"1152411","NYSM-00459":"1122829","NYSM-00460":"1265361","NYSM-00461":"1084294","NYSM-00462":"936605","NYSM-00463":"1479830","NYSM-00464":"1698198","NYSM-00465":"1801787","NYSM-00466":"1359030","NYSM-00467":"1527201","NYSM-00468":"1723054","NYSM-00469":"2226730","NYSM-00470":"2195119","NYSM-00471":"1981205","NYSM-00472":"2455555","NYSM-00473":"2157923","NYSM-00474":"2141772","NYSM-00475":"2115271","NYSM-00476":"2745763","NYSM-00477":"1930656","NYSM-00478":"1454093","NYSM-00479":"929898","NYSM-00480":"1378712","NYSM-00481":"1076505","NYSM-00482":"1231610","NYSM-00483":"1156255","NYSM-00484":"1148476","NYSM-00485":"982970","NYSM-00486":"1356402","NYSM-00487":"1192704","NYSM-00488":"1491937","NYSM-00489":"993709","NYSM-00490":"1436316","NYSM-00491":"843150","NYSM-00492":"987832","NYSM-00493":"968845","NYSM-00494":"855424","NYSM-00495":"1056478","NYSM-00496":"639244","NYSM-00497":"1169925","NYSM-00498":"1513410","NYSM-00499":"809695","NYSM-00500":"1172793","NYSM-00501":"896951","NYSM-00502":"1000092","NYSM-00503":"658234","NYSM-00504":"846064","NYSM-00505":"910122"},{"Metabolite":"1-arachidonylglycerol (20:4)","NYSM-00454":"","NYSM-00455":"1156380","NYSM-00456":"602744","NYSM-00457":"1518558","NYSM-00458":"1829627","NYSM-00459":"1114124","NYSM-00460":"1073183","NYSM-00461":"","NYSM-00462":"858791","NYSM-00463":"999575","NYSM-00464":"","NYSM-00465":"329721","NYSM-00466":"","NYSM-00467":"","NYSM-00468":"","NYSM-00469":"","NYSM-00470":"383462","NYSM-00471":"427053","NYSM-00472":"","NYSM-00473":"550772","NYSM-00474":"484858","NYSM-00475":"","NYSM-00476":"676482","NYSM-00477":"","NYSM-00478":"1076947","NYSM-00479":"772349","NYSM-00480":"1034719","NYSM-00481":"695554","NYSM-00482":"4207625","NYSM-00483":"773040","NYSM-00484":"852651","NYSM-00485":"830401","NYSM-00486":"911580","NYSM-00487":"1597187","NYSM-00488":"687824","NYSM-00489":"925479","NYSM-00490":"714082","NYSM-00491":"1082776","NYSM-00492":"3010703","NYSM-00493":"1169206","NYSM-00494":"2200014","NYSM-00495":"615376","NYSM-00496":"1077022","NYSM-00497":"1536953","NYSM-00498":"1269271","NYSM-00499":"3270167","NYSM-00500":"1732407","NYSM-00501":"1622455","NYSM-00502":"1824959","NYSM-00503":"1537195","NYSM-00504":"1298671","NYSM-00505":"2165461"},{"Metabolite":"1-docosahexaenoylglycerol 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}

}