{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002271","ANALYSIS_ID":"AN003712","VERSION":"1","CREATED_ON":"02-08-2024"}, "PROJECT":{"PROJECT_TITLE":"Glucose metabolism during Xenopus Regeneration","PROJECT_SUMMARY":"Targeted metabolomics of Xenopus tropicalis to study glucose metabolism during regeneration","INSTITUTE":"University of Washington","DEPARTMENT":"Biochemistry","LABORATORY":"Wills Lab","LAST_NAME":"Patel","FIRST_NAME":"Jeet","ADDRESS":"1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA","EMAIL":"pateljeet1224@gmail.com","PHONE":"2065431748","FUNDING_SOURCE":"Royalty Research Fund, 1R01NS099124 from NINDS","DOI":"http://dx.doi.org/10.21228/M81Q5B"}, "STUDY":{"STUDY_TITLE":"Xenopus tropicalis regeneration timecourse","STUDY_SUMMARY":"To identify changes in metabolites that correlate with progression of tail regeneration, we collected a timecourse of tissues containing 250 um of tissue anterior to the wound site as well as all regenerating tissue at 0, 3, and 24 hours post amputation. We also collected the posterior 500 um of the developing tail to represent the metabolic profile of uninjured tissues. Tissues from 25 individuals were collected and frozen in more than 5-8 minutes per replicate before processing as in the methods. 104 metabolites were identified in these samples and relative peak intensities were compared to identify changes in abundance corresponding to regeneration. 42 differentially abundant metabolites were found using MetaboAnalyst, the majority of which were increased 24 hours post amputation. Further investigation of these 24 hours post amputation enriched metabolites revealed that these metabolites were largely associated with increased growth and nucleotide metabolism. This finding is in line with the growth of new tissue seen at this timepoint and also suggests that generation of nucleotides are a major factor in sustaining this growth.","INSTITUTE":"University of Washington","LAST_NAME":"Patel","FIRST_NAME":"Jeet","ADDRESS":"1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA","EMAIL":"pateljeet1224@gmail.com","PHONE":"2065431748","SUBMIT_DATE":"2022-08-03"}, "SUBJECT":{"SUBJECT_TYPE":"Other organism","SUBJECT_SPECIES":"Xenopus tropicalis","AGE_OR_AGE_RANGE":"Stage 41-43"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"21", "Sample ID":"0hpa_B", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"B","RAW_FILE_NAME":"2021-10-15_Wills-38-21_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-21_NEG.mzML"} }, { "Subject ID":"28", "Sample ID":"0hpa_G", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"G","RAW_FILE_NAME":"2021-10-15_Wills-38-28_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-28_NEG.mzML"} }, { "Subject ID":"11", "Sample ID":"0hpa_K", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"K","RAW_FILE_NAME":"2021-10-15_Wills-38-11_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-11_NEG.mzML"} }, { "Subject ID":"35", "Sample ID":"0hpa_L", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"L","RAW_FILE_NAME":"2021-10-15_Wills-38-35_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-35_NEG.mzML"} }, { "Subject ID":"16", "Sample ID":"0hpa_M", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"M","RAW_FILE_NAME":"2021-10-15_Wills-38-16_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-16_NEG.mzML"} }, { "Subject ID":"24", "Sample ID":"0hpa_O", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"O","RAW_FILE_NAME":"2021-10-15_Wills-38-24_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-24_NEG.mzML"} }, { "Subject ID":"2", "Sample ID":"0hpa_P", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"P","RAW_FILE_NAME":"2021-10-15_Wills-38-2_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-2_NEG.mzML"} }, { "Subject ID":"31", "Sample ID":"0hpa_R", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"R","RAW_FILE_NAME":"2021-10-15_Wills-38-31_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-31_NEG.mzML"} }, { "Subject ID":"27", "Sample ID":"0hpa_S", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"S","RAW_FILE_NAME":"2021-10-15_Wills-38-27_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-27_NEG.mzML"} }, { "Subject ID":"25", "Sample ID":"0hpa_T", "Factors":{"Timepoint":"0hpa"}, "Additional sample data":{"Replicate_ID":"T","RAW_FILE_NAME":"2021-10-15_Wills-38-25_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-25_NEG.mzML"} }, { "Subject ID":"37", "Sample ID":"24hpa_K", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"K","RAW_FILE_NAME":"2021-10-15_Wills-38-37_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-37_NEG.mzML"} }, { "Subject ID":"20", "Sample ID":"24hpa_L", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"L","RAW_FILE_NAME":"2021-10-15_Wills-38-20_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-20_NEG.mzML"} }, { "Subject ID":"32", "Sample ID":"24hpa_M", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"M","RAW_FILE_NAME":"2021-10-15_Wills-38-32_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-32_NEG.mzML"} }, { "Subject ID":"22", "Sample ID":"24hpa_O", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"O","RAW_FILE_NAME":"2021-10-15_Wills-38-22_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-22_NEG.mzML"} }, { "Subject ID":"5", "Sample ID":"24hpa_P", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"P","RAW_FILE_NAME":"2021-10-15_Wills-38-5_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-5_NEG.mzML"} }, { "Subject ID":"10", "Sample ID":"24hpa_R", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"R","RAW_FILE_NAME":"2021-10-15_Wills-38-10_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-10_NEG.mzML"} }, { "Subject ID":"8", "Sample ID":"24hpa_S", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"S","RAW_FILE_NAME":"2021-10-15_Wills-38-8_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-8_NEG.mzML"} }, { "Subject ID":"17", "Sample ID":"24hpa_T", "Factors":{"Timepoint":"24hpa"}, "Additional sample data":{"Replicate_ID":"T","RAW_FILE_NAME":"2021-10-15_Wills-38-17_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-17_NEG.mzML"} }, { "Subject ID":"12", "Sample ID":"3hpa_B", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"B","RAW_FILE_NAME":"2021-10-15_Wills-38-12_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-12_NEG.mzML"} }, { "Subject ID":"23", "Sample ID":"3hpa_G", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"G","RAW_FILE_NAME":"2021-10-15_Wills-38-23_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-23_NEG.mzML"} }, { "Subject ID":"26", "Sample ID":"3hpa_K", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"K","RAW_FILE_NAME":"2021-10-15_Wills-38-26_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-26_NEG.mzML"} }, { "Subject ID":"4", "Sample ID":"3hpa_L", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"L","RAW_FILE_NAME":"2021-10-15_Wills-38-4_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-4_NEG.mzML"} }, { "Subject ID":"9", "Sample ID":"3hpa_M", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"M","RAW_FILE_NAME":"2021-10-15_Wills-38-9_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-9_NEG.mzML"} }, { "Subject ID":"18", "Sample ID":"3hpa_O", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"O","RAW_FILE_NAME":"2021-10-15_Wills-38-18_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-18_NEG.mzML"} }, { "Subject ID":"30", "Sample ID":"3hpa_P", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"P","RAW_FILE_NAME":"2021-10-15_Wills-38-30_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-30_NEG.mzML"} }, { "Subject ID":"14", "Sample ID":"3hpa_R", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"R","RAW_FILE_NAME":"2021-10-15_Wills-38-14_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-14_NEG.mzML"} }, { "Subject ID":"6", "Sample ID":"3hpa_S", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"S","RAW_FILE_NAME":"2021-10-15_Wills-38-6_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-6_NEG.mzML"} }, { "Subject ID":"7", "Sample ID":"3hpa_T", "Factors":{"Timepoint":"3hpa"}, "Additional sample data":{"Replicate_ID":"T","RAW_FILE_NAME":"2021-10-15_Wills-38-7_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-7_NEG.mzML"} }, { "Subject ID":"29", "Sample ID":"Tips_B", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"B","RAW_FILE_NAME":"2021-10-15_Wills-38-29_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-29_NEG.mzML"} }, { "Subject ID":"33", "Sample ID":"Tips_G", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"G","RAW_FILE_NAME":"2021-10-15_Wills-38-33_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-33_NEG.mzML"} }, { "Subject ID":"15", "Sample ID":"Tips_K", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"K","RAW_FILE_NAME":"2021-10-15_Wills-38-15_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-15_NEG.mzML"} }, { "Subject ID":"19", "Sample ID":"Tips_L", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"L","RAW_FILE_NAME":"2021-10-15_Wills-38-19_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-19_NEG.mzML"} }, { "Subject ID":"3", "Sample ID":"Tips_M", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"M","RAW_FILE_NAME":"2021-10-15_Wills-38-3_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-3_NEG.mzML"} }, { "Subject ID":"13", "Sample ID":"Tips_O", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"O","RAW_FILE_NAME":"2021-10-15_Wills-38-13_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-13_NEG.mzML"} }, { "Subject ID":"38", "Sample ID":"Tips_P", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"P","RAW_FILE_NAME":"2021-10-15_Wills-38-38_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-38_NEG.mzML"} }, { "Subject ID":"1", "Sample ID":"Tips_R", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"R","RAW_FILE_NAME":"2021-10-15_Wills-38-1_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-1_NEG.mzML"} }, { "Subject ID":"34", "Sample ID":"Tips_S", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"S","RAW_FILE_NAME":"2021-10-15_Wills-38-34_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-34_NEG.mzML"} }, { "Subject ID":"36", "Sample ID":"Tips_T", "Factors":{"Timepoint":"Tips"}, "Additional sample data":{"Replicate_ID":"T","RAW_FILE_NAME":"2021-10-15_Wills-38-36_POS.mzML","RAW_FILE_NAME":"2021-10-15_Wills-38-36_NEG.mzML"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Tadpoles were anesthetized with 0.05% MS-222 in 1/9x MR and tested for response to touch prior to tissue collection. For uninjured tips (Tips), a sterilized scalpel was used to amputate 500µm of the posterior tip. For 0 hours post amputation (hpa) samples, the posterior third of the tail was amputated followed by collection of tail tissue 250µm anterior to the initial wound. For 3 and 24hpa, 250µm of tissue, including the regenerating tissue, was collected. 10 replicates of 25 tails (8 replicates for the 24hpa timepoint) were collected. For each sample, media was removed, and samples were frozen on dry ice within 5-8 minutes from the first amputation.","SAMPLE_TYPE":"Tails"}, "TREATMENT":{"TREATMENT_SUMMARY":"No applicable"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Aqueous metabolites for targeted LC-MS analysis were extracted using a protein precipitation method similar to the one described elsewhere (Mathon et al., 2019; Meador et al., 2020). Samples were first homogenized in 200 µL purified deionized water at 4 ˚C, and then 800 µL of methanol containing 6C13-glucose and 2C13-glutamate (reference internal standards) was added. Afterwards samples were vortexed, stored for 30 minutes at -20 ˚C, sonicated in an ice bath for 10 minutes, centrifuged for 15 min at 14,000 rpm and 4 ˚C, and then 600 µL of supernatant was collected from each sample. Lastly, recovered supernatants were dried on a SpeedVac and reconstituted in 1.0 mL of LC-matching solvent containing 2C13-tyrosine and 3C13-lactate (reference internal standards).","SAMPLEPREP_PROTOCOL_FILENAME":"JPatel_LC-MS_Methods.pdf"}, "CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Shimadzu Nexera X2","COLUMN_NAME":"Waters XBridge BEH Amide XP","CHROMATOGRAPHY_TYPE":"HILIC"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"JPatel_LC-MS_Methods.pdf"}, "MS":{"INSTRUMENT_NAME":"ABI Sciex 6500+","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","MS_COMMENTS":"MS data acquisition was performed in multiple-reaction-monitoring (MRM) mode. LC-MS system was controlled using AB Sciex Analyst 1.6.3 software. Measured MS peaks were integrated using AB Sciex MultiQuant 3.0.3 software. The LC-MS assay was targeting 361 metabolites (plus 4 spiked reference internal standards).","ION_MODE":"POSITIVE"}, "MS_METABOLITE_DATA":{ "Units":"Peak Intensity", 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