#METABOLOMICS WORKBENCH Karin_20200910_054043_mwtab.txt DATATRACK_ID:2160 STUDY_ID:ST001481 ANALYSIS_ID:AN002458 PROJECT_ID:000000 VERSION 1 CREATED_ON September 11, 2020, 12:06 am #PROJECT PR:PROJECT_TITLE Ndufs4 KO mouse model metabolomics studies PR:PROJECT_TYPE Multi-platform metabolomics analysis PR:PROJECT_SUMMARY Multi-platform metabolomics analysis of tissues and biofluids from the Ndufs4 PR:PROJECT_SUMMARY knockout (Ndufs4-/-) mouse model of human Leigh syndrome PR:INSTITUTE North-West University PR:LAST_NAME Louw PR:FIRST_NAME Roan PR:ADDRESS Hofman Street PR:EMAIL Roan.Louw@nwu.ac.za PR:PHONE +27 18 299 4074 #STUDY ST:STUDY_TITLE Metabolomics of Ndufs4 KO brain regions (part - II) ST:STUDY_SUMMARY Targeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT ST:STUDY_SUMMARY mouse anterior cortex (AC) ST:INSTITUTE North-West University ST:LAST_NAME Louw ST:FIRST_NAME Roan ST:ADDRESS Hofman Street ST:EMAIL Roan.Louw@nwu.ac.za ST:PHONE +27 18 299 4074 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENOTYPE_STRAIN Ndufs4, https://www.jax.org/strai n/02705 8 SU:AGE_OR_AGE_RANGE 45-50 days SU:GENDER Male SU:ANIMAL_ANIMAL_SUPPLIER Jackson Laboratory (ME, USA) SU:ANIMAL_LIGHT_CYCLE 12:12 h SU:ANIMAL_FEED Rodent Breeder, Cat. #RM1845, LabChef, Nutritionhub SU:ANIMAL_WATER ad libitum #FACTORS #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - AC1 1 Genotype:WT RAW_FILE_NAME=AC1 1_1.peg SUBJECT_SAMPLE_FACTORS - AC1 2 Genotype:WT RAW_FILE_NAME=AC1 2_1.peg SUBJECT_SAMPLE_FACTORS - AC1 4 Genotype:WT RAW_FILE_NAME=AC1 4_1.peg SUBJECT_SAMPLE_FACTORS - AC1 5 Genotype:WT RAW_FILE_NAME=AC1 5_1.peg SUBJECT_SAMPLE_FACTORS - AC1 7 Genotype:WT RAW_FILE_NAME=AC1 7_1.peg SUBJECT_SAMPLE_FACTORS - AC1 8 Genotype:WT RAW_FILE_NAME=AC1 8_1.peg SUBJECT_SAMPLE_FACTORS - AC1 9 Genotype:WT RAW_FILE_NAME=AC1 9_1.peg SUBJECT_SAMPLE_FACTORS - AC1 11 Genotype:WT RAW_FILE_NAME=AC1 11_1.peg SUBJECT_SAMPLE_FACTORS - AC1 12 Genotype:WT RAW_FILE_NAME=AC1 12_1.peg SUBJECT_SAMPLE_FACTORS - AC1 13 Genotype:WT RAW_FILE_NAME=AC1 13_1.peg SUBJECT_SAMPLE_FACTORS - AC1 17 Genotype:WT RAW_FILE_NAME=AC1 17_1.peg SUBJECT_SAMPLE_FACTORS - AC1 18 Genotype:WT RAW_FILE_NAME=AC1 18_1.peg SUBJECT_SAMPLE_FACTORS - AC1 20 Genotype:WT RAW_FILE_NAME=AC1 20_1.peg SUBJECT_SAMPLE_FACTORS - AC1 22 Genotype:WT RAW_FILE_NAME=AC1 22_1.peg SUBJECT_SAMPLE_FACTORS - AC1 23 Genotype:WT RAW_FILE_NAME=AC1 23_1.peg SUBJECT_SAMPLE_FACTORS - AC2 25 Genotype:WT RAW_FILE_NAME=AC2 25_1.peg SUBJECT_SAMPLE_FACTORS - AC2 26 Genotype:WT RAW_FILE_NAME=AC2 26_1.peg SUBJECT_SAMPLE_FACTORS - AC2 28 Genotype:WT RAW_FILE_NAME=AC2 28_1.peg SUBJECT_SAMPLE_FACTORS - AC2 30 Genotype:WT RAW_FILE_NAME=AC2 30_1.peg SUBJECT_SAMPLE_FACTORS - AC2 31 Genotype:WT RAW_FILE_NAME=AC2 31_1.peg SUBJECT_SAMPLE_FACTORS - AC2 37 Genotype:WT RAW_FILE_NAME=AC2 37_1.peg SUBJECT_SAMPLE_FACTORS - AC2 39 Genotype:WT RAW_FILE_NAME=AC2 39_1.peg SUBJECT_SAMPLE_FACTORS - AC2 40 Genotype:WT RAW_FILE_NAME=AC2 40_1.peg SUBJECT_SAMPLE_FACTORS - AC2 E 3 Genotype:WT RAW_FILE_NAME=AC2 Extract 3_1.peg SUBJECT_SAMPLE_FACTORS - AC2 E 6 Genotype:WT RAW_FILE_NAME=AC2 Extract 6_1.peg SUBJECT_SAMPLE_FACTORS - AC1 3 Genotype:KO RAW_FILE_NAME=AC1 3_1.peg SUBJECT_SAMPLE_FACTORS - AC1 10 Genotype:KO RAW_FILE_NAME=AC1 10_1.peg SUBJECT_SAMPLE_FACTORS - AC1 14 Genotype:KO RAW_FILE_NAME=AC1 14_1.peg SUBJECT_SAMPLE_FACTORS - AC1 15 Genotype:KO RAW_FILE_NAME=AC1 15_1.peg SUBJECT_SAMPLE_FACTORS - AC1 16 Genotype:KO RAW_FILE_NAME=AC1 16_1.peg SUBJECT_SAMPLE_FACTORS - AC1 19 Genotype:KO RAW_FILE_NAME=AC1 19_1.peg SUBJECT_SAMPLE_FACTORS - AC1 21 Genotype:KO RAW_FILE_NAME=AC1 21_1.peg SUBJECT_SAMPLE_FACTORS - AC1 24 Genotype:KO RAW_FILE_NAME=AC1 24_1.peg SUBJECT_SAMPLE_FACTORS - AC2 27 Genotype:KO RAW_FILE_NAME=AC2 27_1.peg SUBJECT_SAMPLE_FACTORS - AC2 29 Genotype:KO RAW_FILE_NAME=AC2 29_1.peg SUBJECT_SAMPLE_FACTORS - AC2 32 Genotype:KO RAW_FILE_NAME=AC2 32_1.peg SUBJECT_SAMPLE_FACTORS - AC2 33 Genotype:KO RAW_FILE_NAME=AC2 33_1.peg SUBJECT_SAMPLE_FACTORS - AC2 34 Genotype:KO RAW_FILE_NAME=AC2 34_1.peg SUBJECT_SAMPLE_FACTORS - AC2 35 Genotype:KO RAW_FILE_NAME=AC2 35_1.peg SUBJECT_SAMPLE_FACTORS - AC2 36 Genotype:KO RAW_FILE_NAME=AC2 36_1.peg SUBJECT_SAMPLE_FACTORS - AC2 38 Genotype:KO RAW_FILE_NAME=AC2 38_1.peg SUBJECT_SAMPLE_FACTORS - AC2 41 Genotype:KO RAW_FILE_NAME=AC2 41_1.peg SUBJECT_SAMPLE_FACTORS - AC2 42 Genotype:KO RAW_FILE_NAME=AC2 42_1.peg SUBJECT_SAMPLE_FACTORS - AC2 E 1 Genotype:KO RAW_FILE_NAME=AC2 Extract 1_1.peg SUBJECT_SAMPLE_FACTORS - AC2 E 2 Genotype:KO RAW_FILE_NAME=AC2 Extract 2_1.peg SUBJECT_SAMPLE_FACTORS - AC2 E 5 Genotype:KO RAW_FILE_NAME=AC2 Extract 5_1.peg #COLLECTION CO:COLLECTION_SUMMARY Mice were euthanized between postnatal day (P) 45-50 via cervical dislocation at CO:COLLECTION_SUMMARY the same time of day (8:00-9:00 AM) after overnight (12-h) fasting. The brain CO:COLLECTION_SUMMARY was removed and rinsed with saline solution (SABAX PBS; 0.9% NaCl (w/v), #7634, CO:COLLECTION_SUMMARY Adcock Ingram) to remove surrounding blood. The brain regions of interest, CO:COLLECTION_SUMMARY namely the anterior cortex (AC), brainstem (BS), cerebellum (CB) and olfactory CO:COLLECTION_SUMMARY bulbs (OB), were then dissected, snap-frozen in liquid nitrogen (within 15 CO:COLLECTION_SUMMARY minutes postmortem) and stored at − 80°C until used. CO:SAMPLE_TYPE Brain #TREATMENT TR:TREATMENT_SUMMARY The animals did not receive any treatment #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Brain regions were homogenized in the presence of internal standards using a SP:SAMPLEPREP_SUMMARY vibration mill. Metabolite extraction was achieved using a modified monophasic SP:SAMPLEPREP_SUMMARY Bligh–Dyer extraction method with a solvent ratio of 3:1:1 SP:SAMPLEPREP_SUMMARY (methanol:water:chloroform). #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent 7890A CH:COLUMN_NAME Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Leco Pegasus HT TOF MS:INSTRUMENT_TYPE GC-TOF MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:MS_COMMENTS The LECO Corporation ChromaTOF® software (v 4.5x) was used for data acquisition MS:MS_COMMENTS and extraction. This included automatic baseline removal via the “spanning” MS:MS_COMMENTS tracking method (offset of 1; just above the noise) and auto smoothing, with the MS:MS_COMMENTS software’s Statistical Compare feature used to align peaks. Spectral matching MS:MS_COMMENTS was done using the NIST11 commercial library and an in-house mass spectral MS:MS_COMMENTS library in order to identify important analytes. MS:MS_RESULTS_FILE ST001481_AN002458_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Seconds #END