{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003269","ANALYSIS_ID":"AN005355","PROJECT_ID":"PR002030","VERSION":"1","CREATED_ON":"June 18, 2024, 9:50 am"}, "PROJECT":{"PROJECT_TITLE":"Metabolomic changes in mouse tissues following modulation of serine through the diet","PROJECT_SUMMARY":"We analyzed metabolites in the retina, choroid/RPE, and plasma from WT and PHGDH heterozygous mice that were fed either a control or serine/glycine-deprived diet. Additionally, we also analyzed metabolites from the retina, choroid/RPE, paw skin, and plasma from mice that were previously on either a control or serine/glycine-deprived diet and then switched back to a control or serine-supplemented diet.","INSTITUTE":"Salk Institute","DEPARTMENT":"Molecular and Cell Biology Laboratory","LABORATORY":"Metallo Lab","LAST_NAME":"Lim","FIRST_NAME":"Esther","ADDRESS":"10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA","EMAIL":"ewlim2024@gmail.com","PHONE":"(858) 453-4100","FUNDING_SOURCE":"R01CA234245"}, "STUDY":{"STUDY_TITLE":"WT and PHGDH(+/-) mice fed control or -SG diet","STUDY_SUMMARY":"We analyzed metabolites in the retina, choroid/RPE, and plasma from WT and PHGDH heterozygous mice that were fed either a control or serine/glycine-deprived diet.","INSTITUTE":"Salk Institute for Biological Studies","LAST_NAME":"Lim","FIRST_NAME":"Esther","ADDRESS":"10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA","EMAIL":"ewlim2024@gmail.com","PHONE":"(858) 453-4100","NUM_GROUPS":"4","TOTAL_SUBJECTS":"20","NUM_MALES":"20"}, "SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"12-16 weeks","WEIGHT_OR_WEIGHT_RANGE":"20-30g","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"Phgdh floxed/floxed from the Shigeki Furuya Lab; E2a-Cre mice from JAX","ANIMAL_HOUSING":"5/cage","ANIMAL_LIGHT_CYCLE":"12h dark/12 h light","ANIMAL_FEED":"Special diets; see group labeling","ANIMAL_WATER":"Ad libitum"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"R_L7A", "Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L7A.d"} }, { "Subject ID":"-", "Sample ID":"R_L7B", "Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L7B.d"} }, { "Subject ID":"-", "Sample ID":"R_L7C", "Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L7C.d"} }, { "Subject ID":"-", "Sample ID":"R_L7D", "Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L7D.d"} }, { "Subject ID":"-", "Sample ID":"R_L7E", "Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L7E.d"} }, { "Subject ID":"-", "Sample ID":"R_L8A", "Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L8A.d"} }, { "Subject ID":"-", "Sample ID":"R_L8B", "Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L8B.d"} }, { "Subject ID":"-", "Sample ID":"R_L8C", "Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L8C.d"} }, { "Subject ID":"-", "Sample ID":"R_L8D", "Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L8D.d"} }, { "Subject ID":"-", "Sample ID":"R_L8E", "Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L8E.d"} }, { "Subject ID":"-", "Sample ID":"R_L3A", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L3A.d"} }, { "Subject ID":"-", "Sample ID":"R_L3B", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L3B.d"} }, { "Subject ID":"-", "Sample ID":"R_L3C", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L3C.d"} }, { "Subject ID":"-", "Sample ID":"R_L3D", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L3D.d"} }, { "Subject ID":"-", "Sample ID":"R_L3E", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L3E.d"} }, { "Subject ID":"-", "Sample ID":"R_L4A", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L4A.d"} }, { "Subject ID":"-", "Sample ID":"R_L4B", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L4B.d"} }, { "Subject ID":"-", "Sample ID":"R_L4C", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L4C.d"} }, { "Subject ID":"-", "Sample ID":"R_L4D", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L4D.d"} }, { "Subject ID":"-", "Sample ID":"R_L4E", "Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse retina"}, "Additional sample data":{"RAW_FILE_NAME(Raw file name)":"R_L4E.d"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Tissues were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80 C until analysis","SAMPLE_TYPE":"Retina","STORAGE_CONDITIONS":"-80℃"}, "TREATMENT":{"TREATMENT_SUMMARY":"In this cohort, there were wildtype (WT) and PHGDH heterozygous (PHGDH +/-) mice that were put on either a control amino acid or serine/glycine-depleted diet."}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"For sphingolipid extraction from retina and choroid/RPE, frozen tissue was homogenized with a ball mill (Retsch Mixer Mill MM 400) at 30 Hz for 3 min in 500 μl of −20°C methanol, 400 μl of ice-cold saline, and 100 μl of ice-cold MilliQ water, spiked with deuterated internal standards as described earlier. The mixture was then transferred into a 2-ml Eppendorf tube containing 1 ml of chloroform. The tubes were vortexed for 5 min and centrifuged at 16,000g at 4°C for 5 min. The lower organic phase was collected, and 2 μl of formic acid was added to the remaining polar phase, which was re-extracted with 1 ml of chloroform. Combined organic phases were dried and resuspended in 50 μl of 0.2% formic acid and 1 mM ammonium formate in methanol. Last, the tubes were sonicated in a bath sonicator for 10 min and spun at 16,000g for 10 min at 4°C. For plasma, 50 μl of plasma was extracted with 500 μl of −20°C methanol, 400 μl of saline, and 100 μl of water spiked with deuterated internal standards. Chloroform (1 ml) was then added to the tubes. The tubes were vortexed for 5 min and centrifuged at 16,000g at 4°C for 5 min. The lower organic phase was collected, and 2 μl of formic acid was added to the remaining polar phase, which was reextracted with 1 ml of chloroform. Combined organic phases were dried and resuspended in 100 μl of 0.2% formic acid and 1 mM ammonium formate in methanol. Next, the tubes were sonicated in a bath sonicator for 10 min and spun at 16,000g for 10 min at 4°C","PROCESSING_STORAGE_CONDITIONS":"Room temperature","EXTRACT_STORAGE":"4℃"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The gradient elution program consisted of the following profile: 0 min, 82% B; 3 min, 82% B; 4 min, 90% B, 18 min, 99% B; 25 min, 99%, 27 min, 82% B, 30 min, 82% B.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6460","COLUMN_NAME":"Peeke Scientific Spectra 3um C8SR (150 x 3mm)","SOLVENT_A":"100% water; 0.2% formic acid; 2 mM ammonium formate","SOLVENT_B":"100% methanol; 0.2% formic acid; 1 mM ammonium formate","FLOW_GRADIENT":"0 min, 82% B; 3 min, 82% B; 4 min, 90% B; 18 min, 99% B; 25 min, 99%; 27 min, 82% B; and 30 min, 82% B","FLOW_RATE":"0.5 mL/min","COLUMN_TEMPERATURE":"40"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS"}, "MS":{"INSTRUMENT_NAME":"Agilent 6460 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Software: Agilent MassHunter Sphingolipid species were analyzed by selective reaction monitoring of the transition from precursor to product ions at associated optimized collision energies, and fragmentor voltages are provided elsewhere (https://doi.org/10.1007/978-1-60761-322-0_22). The m/z values of the precursor and product ions are provided in the following format: Precursor ion -> Product ion."}, "MS_METABOLITE_DATA":{ "Units":"Normalized ion count/mg of protein", "Data":[{"Metabolite":"Cer 18:1/16:0","R_L7A":"218.3249371","R_L7B":"264.5602392","R_L7C":"259.1481876","R_L7D":"238.9299685","R_L7E":"269.1016078","R_L8A":"294.0006208","R_L8B":"351.2620854","R_L8C":"260.1358587","R_L8D":"240.9111265","R_L8E":"258.4676585","R_L3A":"225.5061526","R_L3B":"284.0503822","R_L3C":"195.9975103","R_L3D":"220.6400462","R_L3E":"262.3347478","R_L4A":"264.2073214","R_L4B":"209.2723446","R_L4C":"222.938899","R_L4D":"282.8070776","R_L4E":"300.8868754"},{"Metabolite":"Cer 18:1/18:0","R_L7A":"95.67839047","R_L7B":"94.98033858","R_L7C":"122.3945517","R_L7D":"103.9294654","R_L7E":"102.2959109","R_L8A":"96.43445302","R_L8B":"151.1074368","R_L8C":"93.35542252","R_L8D":"115.6205948","R_L8E":"109.4211568","R_L3A":"117.442205","R_L3B":"131.281687","R_L3C":"110.0756198","R_L3D":"132.0010795","R_L3E":"113.3971304","R_L4A":"127.5465558","R_L4B":"110.8150351","R_L4C":"115.1873665","R_L4D":"107.5562162","R_L4E":"129.4593084"},{"Metabolite":"Cer 18:1/20:0","R_L7A":"565.871391","R_L7B":"585.0575158","R_L7C":"716.0143085","R_L7D":"594.2504418","R_L7E":"609.4636551","R_L8A":"602.564407","R_L8B":"907.3166298","R_L8C":"657.9702986","R_L8D":"656.9646747","R_L8E":"459.8490032","R_L3A":"769.8451438","R_L3B":"586.6024728","R_L3C":"442.6334644","R_L3D":"692.9041283","R_L3E":"674.6728387","R_L4A":"580.4983356","R_L4B":"585.1882466","R_L4C":"589.9917503","R_L4D":"640.8875512","R_L4E":"714.2513523"},{"Metabolite":"Cer 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18:1/24:1","R_L7A":"247.7506231","R_L7B":"280.3060676","R_L7C":"337.2958394","R_L7D":"271.0364712","R_L7E":"267.4916527","R_L8A":"266.7019218","R_L8B":"367.9960627","R_L8C":"252.1138913","R_L8D":"292.5525295","R_L8E":"248.3124194","R_L3A":"343.4972833","R_L3B":"266.6569888","R_L3C":"194.1976355","R_L3D":"287.1917993","R_L3E":"273.6568617","R_L4A":"272.7104251","R_L4B":"282.6509834","R_L4C":"251.0657498","R_L4D":"252.0931918","R_L4E":"264.2075321"},{"Metabolite":"DHCer 18:0/16:0","R_L7A":"1.723290058","R_L7B":"1.732633783","R_L7C":"1.772952397","R_L7D":"1.755924016","R_L7E":"1.85638973","R_L8A":"1.823863322","R_L8B":"1.835998793","R_L8C":"2.025956135","R_L8D":"1.809926792","R_L8E":"3.104324661","R_L3A":"1.965585093","R_L3B":"1.836802666","R_L3C":"2.460470943","R_L3D":"1.483135633","R_L3E":"1.493520822","R_L4A":"1.75440094","R_L4B":"1.459659446","R_L4C":"1.518400529","R_L4D":"1.894446296","R_L4E":"1.872480967"},{"Metabolite":"DHCer 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