{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001481","ANALYSIS_ID":"AN002458","VERSION":"1","CREATED_ON":"September 11, 2020, 12:06 am"}, "PROJECT":{"PROJECT_TITLE":"Ndufs4 KO mouse model metabolomics studies","PROJECT_TYPE":"Multi-platform metabolomics analysis","PROJECT_SUMMARY":"Multi-platform metabolomics analysis of tissues and biofluids from the Ndufs4 knockout (Ndufs4-/-) mouse model of human Leigh syndrome","INSTITUTE":"North-West University","LAST_NAME":"Louw","FIRST_NAME":"Roan","ADDRESS":"Hofman Street","EMAIL":"Roan.Louw@nwu.ac.za","PHONE":"+27 18 299 4074"}, "STUDY":{"STUDY_TITLE":"Metabolomics of Ndufs4 KO brain regions (part - II)","STUDY_SUMMARY":"Targeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT mouse anterior cortex (AC)","INSTITUTE":"North-West University","LAST_NAME":"Louw","FIRST_NAME":"Roan","ADDRESS":"Hofman Street","EMAIL":"Roan.Louw@nwu.ac.za","PHONE":"+27 18 299 4074"}, "SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"Ndufs4, https://www.jax.org/strai n/02705 8","AGE_OR_AGE_RANGE":"45-50 days","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratory (ME, USA)","ANIMAL_LIGHT_CYCLE":"12:12 h","ANIMAL_FEED":"Rodent Breeder, Cat. #RM1845, LabChef, Nutritionhub","ANIMAL_WATER":"ad libitum"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"AC1 1", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 1_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 2", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 2_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 4", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 4_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 5", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 5_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 7", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 7_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 8", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 8_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 9", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 9_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 11", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 11_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 12", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 12_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 13", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 13_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 17", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 17_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 18", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 18_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 20", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 20_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 22", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 22_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 23", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 23_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 25", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 25_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 26", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 26_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 28", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 28_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 30", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 30_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 31", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 31_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 37", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 37_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 39", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 39_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 40", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 40_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 E 3", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 Extract 3_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 E 6", "Factors":{"Genotype":"WT"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 Extract 6_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 3", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 3_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 10", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 10_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 14", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 14_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 15", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 15_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 16", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 16_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 19", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 19_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 21", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 21_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC1 24", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC1 24_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 27", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 27_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 29", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 29_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 32", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 32_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 33", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 33_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 34", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 34_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 35", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 35_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 36", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 36_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 38", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 38_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 41", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 41_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 42", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 42_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 E 1", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 Extract 1_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 E 2", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 Extract 2_1.peg"} }, { "Subject ID":"-", "Sample ID":"AC2 E 5", "Factors":{"Genotype":"KO"}, "Additional sample data":{"RAW_FILE_NAME":"AC2 Extract 5_1.peg"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Mice were euthanized between postnatal day (P) 45-50 via cervical dislocation at the same time of day (8:00-9:00 AM) after overnight (12-h) fasting. The brain was removed and rinsed with saline solution (SABAX PBS; 0.9% NaCl (w/v), #7634, Adcock Ingram) to remove surrounding blood. The brain regions of interest, namely the anterior cortex (AC), brainstem (BS), cerebellum (CB) and olfactory bulbs (OB), were then dissected, snap-frozen in liquid nitrogen (within 15 minutes postmortem) and stored at − 80°C until used.","SAMPLE_TYPE":"Brain"}, "TREATMENT":{"TREATMENT_SUMMARY":"The animals did not receive any treatment"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a modified monophasic Bligh–Dyer extraction method with a solvent ratio of 3:1:1 (methanol:water:chloroform)."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Leco Pegasus HT TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"The LECO Corporation ChromaTOF® software (v 4.5x) was used for data acquisition and extraction. This included automatic baseline removal via the “spanning” tracking method (offset of 1; just above the noise) and auto smoothing, with the software’s Statistical Compare feature used to align peaks. Spectral matching was done using the NIST11 commercial library and an in-house mass spectral library in order to identify important analytes.","MS_RESULTS_FILE":"ST001481_AN002458_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Seconds"} }