{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001486","ANALYSIS_ID":"AN002463","VERSION":"1","CREATED_ON":"September 15, 2020, 12:43 pm"},

"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 - VI)","STUDY_SUMMARY":"Untargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse cerebellum (CB)","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":"CBA 1 (25)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 1 (25)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 2 (26)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 2 (26)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 4 (28)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 4 (28)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 6 (30)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 6 (30)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 9 (1)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 9 (1)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 10 (2)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 10 (2)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 12 (4)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 12 (4)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 14 (5)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 14 (5)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 16 (7)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 16 (7)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 17 (8)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 17 (8)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 18 (9)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 18 (9)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 19 (11)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 19 (11)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 22 (37)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 22 (37)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 24 (39) reg",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 24 (39) reg_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 25 (40)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 25 (40)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 28 (E6)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 28 (E6)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 31 (E3)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 31 (E3)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 34 (12)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 34 (12)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 35 (13)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 35 (13)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 38 (17)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 38 (17)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 39 (18)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 39 (18)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 41 (20)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 41 (20)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 43 (22)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 43 (22)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 44 (23)",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 44 (23)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 3 (27)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 3 (27)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 5 (29)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 5 (29)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 7 (32)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 7 (32)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 8 (33)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 8 (33)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 11 (3)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 11 (3)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 13 (34)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 13 (34)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 15 (35)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 15 (35)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 20 (14)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 20 (14)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 21 (36)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 21 (36)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBA 23 (38)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBA 23 (38)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 26 (41)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 26 (41)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 27 (42)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 27 (42)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 29 (E1)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 29 (E1)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 30 (E2)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 30 (E2)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 32 (E4)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 32 (E4)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 33 (E5)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 33 (E5)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 36 (15)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 36 (15)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 37 (16)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 37 (16)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 40 (19)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 40 (19)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 42 (21)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 42 (21)_1.peg"}
},
{
"Subject ID":"-",
"Sample ID":"CBB 45 (24)",
"Factors":{"Genotype":"KO"},
"Additional sample data":{"RAW_FILE_NAME":"CBB 45 (24)_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).","SAMPLEPREP_PROTOCOL_FILENAME":"GC_sample_prep_protocol.pdf;Data_processing_method.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"Data_processing_method.pdf"},

"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":"ST001486_AN002463_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Seconds"}

}