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}, { "Subject ID":"MOUSE_153", "Sample ID":"345323_153", "Factors":{"Genotype":"Mvk"}, "Additional sample data":{"Gender":"M","zygosity":"+/-"} }, { "Subject ID":"MOUSE_154", "Sample ID":"328195_154", "Factors":{"Genotype":"Mvk"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_155", "Sample ID":"328199_155", "Factors":{"Genotype":"Mvk"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_156", "Sample ID":"349944_156", "Factors":{"Genotype":"Mvk"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_157", "Sample ID":"366627_157", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_158", "Sample ID":"349640_158", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_159", "Sample ID":"349643_159", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_160", "Sample ID":"349745_160", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_161", "Sample ID":"349748_161", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_162", "Sample ID":"349774_162", "Factors":{"Genotype":"Nek2"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_163", "Sample ID":"487174_163", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_164", "Sample ID":"511373_164", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_165", "Sample ID":"511380_165", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_166", "Sample ID":"487277_166", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_167", "Sample ID":"496303_167", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_168", "Sample ID":"496304_168", "Factors":{"Genotype":"Ulk3"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_169", "Sample ID":"237811_169", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"M","zygosity":"+/-"} }, { "Subject ID":"MOUSE_170", "Sample ID":"237812_170", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"M","zygosity":"+/-"} }, { "Subject ID":"MOUSE_171", "Sample ID":"206458_171", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"M","zygosity":"+/-"} }, { "Subject ID":"MOUSE_172", "Sample ID":"248921_172", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_173", "Sample ID":"249730_173", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_174", "Sample ID":"249731_174", "Factors":{"Genotype":"Ptpn12"}, "Additional sample data":{"Gender":"F","zygosity":"+/-"} }, { "Subject ID":"MOUSE_175", "Sample ID":"69286_175", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_176", "Sample ID":"69290_176", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_177", "Sample ID":"73696_177", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"M","zygosity":"-/-"} }, { "Subject ID":"MOUSE_178", "Sample ID":"55771_178", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_179", "Sample ID":"55774_179", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_180", "Sample ID":"55776_180", "Factors":{"Genotype":"Sra1"}, "Additional sample data":{"Gender":"F","zygosity":"-/-"} }, { "Subject ID":"MOUSE_181", "Sample ID":"34419_181", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_182", "Sample ID":"38434_182", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_183", "Sample ID":"38538_183", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_184", "Sample ID":"38541_184", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_185", "Sample ID":"69395_185", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_186", "Sample ID":"91834_186", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_187", "Sample ID":"115757_187", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_188", "Sample ID":"115864_188", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_189", "Sample ID":"55857_189", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_190", "Sample ID":"69499_190", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_191", "Sample ID":"144610_191", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_192", "Sample ID":"187595_192", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_193", "Sample ID":"198313_193", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_194", "Sample ID":"144713_194", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_195", "Sample ID":"170956_195", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_196", "Sample ID":"198416_196", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_197", "Sample ID":"209137_197", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_198", "Sample ID":"229587_198", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_199", "Sample ID":"237610_199", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_200", "Sample ID":"257540_200", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_201", "Sample ID":"281970_201", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_202", "Sample ID":"209241_202", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_203", "Sample ID":"220170_203", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_204", "Sample ID":"229695_204", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_205", "Sample ID":"237716_205", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_206", "Sample ID":"257643_206", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_207", "Sample ID":"307710_207", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_208", "Sample ID":"348926_208", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_209", "Sample ID":"365959_209", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_210", "Sample ID":"296904_210", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_211", "Sample ID":"319741_211", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_212", "Sample ID":"349029_212", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_213", "Sample ID":"410683_213", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_214", "Sample ID":"441144_214", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_215", "Sample ID":"483044_215", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_216", "Sample ID":"417795_216", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_217", "Sample ID":"432639_217", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_218", "Sample ID":"448374_218", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} }, { "Subject ID":"MOUSE_219", "Sample ID":"510073_219", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"M","zygosity":"+/+"} }, { "Subject ID":"MOUSE_220", "Sample ID":"496096_220", "Factors":{"Genotype":"Null"}, "Additional sample data":{"Gender":"F","zygosity":"+/+"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Blood specimens were collected using the IMPC protocol https://www.mousephenotype.org/impress/","SAMPLE_TYPE":"Blood (plasma)"}, "TREATMENT":{"TREATMENT_SUMMARY":"30 genotypes and one group of wildtype mouse"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites were extracted using standard protocols for GCMS and LCMS assays by the West Coast Metabolomics Center."}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Leco Pegasus IV TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Data acquisition : An Agilent 6890 gas chromatography instrument equipped with a Gerstel automatic linear exchange systems (ALEX) which included a multipurpose sample dual rail and a Gerstel cold injection system (CIS). The CIS temperature program was : 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume was 0.5 µL with 10 µL/s injection speed. Injection mode was splitless with a purge time of 25 seconds. Injector liner was changed after every 10 samples. Injection syringe was washed with 10 µL of ethyl acetate before and after each run. A Rtx-5Sil MS column (30m length, 0.25 mm i.d, 0.25 microM 95% dimethyl 5% diphenyl polysiloxane film). An additional 10 m integrated guard column was used. Mobile phase was 99.9999% pure Helium gas with a flow rate of 1ml/min. GC temperature program was : hold at 50°C for 1 min, ramped at 20°C/min to 330°C and then hold for 5 minutes. A Leco Pegasus IV time of flight mass spectrometer was used to acquire data. The transfer line temperature between gas chromatograph and mass spectrometer was set to 280°C. Electron impact ionization at 70V was employed with an ion-source temperature of 250°C. Acquisition rate was 17 spectra/second with a scan mass range of 85-500 Da. Data processing : Data processing Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific *.peg files, as generic *.txt result files and additionally as generic ANDI MS *.cdf files. ChromaTOF vs. 4.0 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result *.txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database.The BinBase algorithm (rtx5) used the settings: validity of chromatogram (10^7 counts s -1 ), unbiased retention index marker detection (MS similarity>800, validity of intensity range for high m/z marker ions), retention index calculation by 5th order polynomial regression. Spectra are cut to 5% base peak abundance and matched to database entries from most to least abundant spectra using the following matching filters: retention index window ±2,000 units (equivalent to about ±2 s retention time), validation of unique ions and apex masses (unique ion must be included in apexing masses and present at >3% of base peak abundance), mass spectrum similarity must fit criteria dependent on peak purity and signal/noise ratios and a final isomer filter. Failed spectra are automatically entered as new database entries if s/n >25, purity 80%. All thresholds reflect settings for ChromaTOF v. 4.0. Quantification is reported as peak height using the unique ion as default, unless a different quantification ion is manually set in the BinBase administration software BinView. A quantification report table is produced for all database entries that are positively detected in more than 10% of the samples of a study design class (as defined in the miniX database) for unidentified metabolites. A subsequent post-processing module is employed to automatically replace missing values from the *.cdf files. Replaced values are labeled as ‘low confidence’ by color coding, and for each metabolite, the number of high-confidence peak detections is recorded as well as the ratio of the average height of replaced values to high-confidence peak detections. 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