{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002275","ANALYSIS_ID":"AN003718","VERSION":"1","CREATED_ON":"August 30, 2022, 1:46 pm"}, "PROJECT":{"PROJECT_TITLE":"Gut-brain axis: Insights from hippocampal neurogenesis and brain tumor development in a mouse model of experimental colitis induced by dextran sodium sulfate","PROJECT_SUMMARY":"We here reported investigations on a model of chemically induced experimental colitis by oral administration of sodium dextran sulfate (DSS) in C57BL/6 mice. We investigated, in vivo, the crosstalk between the intestine and the brain, evaluating the consequences of intestinal inflamma-tion on neuroinflammation and hippocampal adult neurogenesis. By using different DSS admin-istration strategies, we were able to induce acute or chronic colitis simulating clinical character-istics observed in IBD patients","INSTITUTE":"Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile","LAST_NAME":"Lorenzo Rebenaque","FIRST_NAME":"Laura","ADDRESS":"calle seminari sn Alfara del Patriarca","EMAIL":"laura.lorenzorebenaque@uchceu.es","PHONE":"615056012"}, "STUDY":{"STUDY_TITLE":"Insights from hippocampal neurogenesis and brain tumor development in a mouse model of experimental colitis induced by dextran sodium sulfate","STUDY_SUMMARY":"We here reported investigations on a model of chemically induced experimental colitis by oral administration of sodium dextran sulfate (DSS) in C57BL/6 mice. We investigated, in vivo, the crosstalk between the intestine and the brain, evaluating the consequences of intestinal inflamma-tion on neuroinflammation and hippocampal adult neurogenesis. By using different DSS admin-istration strategies, we were able to induce acute or chronic colitis simulating clinical character-istics observed in IBD patients","INSTITUTE":"Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile","LAST_NAME":"Lorenzo Rebenaque","FIRST_NAME":"Laura","ADDRESS":"calle seminari sn Alfara del Patriarca","EMAIL":"laura.lorenzorebenaque@uchceu.es","PHONE":"615056012"}, "SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"UN A WK1 1", "Factors":{"Group":"UN","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK1 1.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK1 2", "Factors":{"Group":"UN","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK1 2.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK1 3", "Factors":{"Group":"UN","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK1 3.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK1 4", "Factors":{"Group":"UN","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK1 4.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK1 5", "Factors":{"Group":"UN","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK1 5.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK1 1", "Factors":{"Group":"DSS","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK1 1.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK1 2", "Factors":{"Group":"DSS","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK1 2.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK1 3", "Factors":{"Group":"DSS","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK1 3.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK1 4", "Factors":{"Group":"DSS","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK1 4.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK1 5", "Factors":{"Group":"DSS","Moment":"7 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK1 5.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK2 1", "Factors":{"Group":"UN","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK2 1.raw"} }, { "Subject ID":"-", "Sample ID":"UN A WK2 2", "Factors":{"Group":"UN","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"UN A WK2 2.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK2 1", "Factors":{"Group":"DSS","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK2 1.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK2 2", "Factors":{"Group":"DSS","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK2 2.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK2 3", "Factors":{"Group":"DSS","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK2 3.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK2 4", "Factors":{"Group":"DSS","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK2 4.raw"} }, { "Subject ID":"-", "Sample ID":"DSS A WK2 5", "Factors":{"Group":"DSS","Moment":"14 ACUTE"}, "Additional sample data":{"RAW_FILE_NAME":"DSS A WK2 5.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 1", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 1.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 2", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 2.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 3", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 3.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 4", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 4.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 5", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 5.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 6", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 6.raw"} }, { "Subject ID":"-", "Sample ID":"UN C 7", "Factors":{"Group":"UN","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"UN C 7.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C1", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C1.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C2", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C2.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C3", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C3.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C4", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C4.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C5", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C5.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C6", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C6.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C7", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C7.raw"} }, { "Subject ID":"-", "Sample ID":"DSS C8", "Factors":{"Group":"DSS","Moment":"CRONICA"}, "Additional sample data":{"RAW_FILE_NAME":"DSS C8.raw"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Fecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment","SAMPLE_TYPE":"Colon"}, "TREATMENT":{"TREATMENT_SUMMARY":"For induction of acute colitis, male mice of 8 weeks of age were administered with a single cycle of 0.7% (w/v) DSS for 7 days followed by 3 or 7 days of DSS-free drinking water. For induction of chronic colitis, male mice of 8 weeks of age were treated with 3 repeated DSS cycles of 7 days each followed by a recovery period of 14 days with DSS-free drinking water."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"A pool of 2 frozen stool samples from 2 independent mice (total dry weigh 15-25mg) from the different experimental groups [UN-Acute n=5; UN-Chronic n= 7; DSS-acute, at the end (n=5) or one week after DSS treatment (n=5) and DSS-chronic (n=8)] were mixed and shacked for two times in 750 l of aqueous solution with 75% of methanol, 0.1% of formic acid and 1ug/ml of formonetin as internal control for 20 min at room temperature. The mixture was then vortexed for 3 min followed by centrifugation at 15 000g for 15 min. The suspension (600μL) was used for metabolic profiling. For the LC-ESI-MS analysis, samples were transferred to HPLC tubes and an aliquot of 3 μL was injected for the analysis. Liquid chromatography coupled to high-resolution mass spectrometry conditions were as pre-viously reported https://www.mdpi.com/1422-0067/22/18/9716."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Q-Exactive","COLUMN_NAME":"C18"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"Other","ION_MODE":"NEGATIVE","MS_COMMENTS":"ESI/APCI. Untargeted metabolomics was performed using the Compound Discovered software (Thermofisher Scientific), which performs chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses (m/z).","MS_RESULTS_FILE":"ST002275_AN003718_Results.txt UNITS:m/z ratio Has m/z:Yes Has RT:Yes RT units:Minutes"} }