{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003270","ANALYSIS_ID":"AN005356","PROJECT_ID":"PR002030","VERSION":"1","CREATED_ON":"June 18, 2024, 10:27 pm"},

"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: Back of eye","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. This study contains back of eye (choroid/RPE) samples.","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/12h light","ANIMAL_FEED":"Special diets; see group labeling","ANIMAL_WATER":"Ad libitum"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"E_L7A",
"Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L7A.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L7B",
"Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L7B.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L7C",
"Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L7C.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L7D",
"Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L7D.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L7E",
"Factors":{"Genotype":"Wild-type","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L7E.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L8A",
"Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L8A.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L8B",
"Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L8B.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L8C",
"Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L8C.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L8D",
"Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L8D.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L8E",
"Factors":{"Genotype":"Wild-type","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L8E.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L3A",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L3A.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L3B",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L3B.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L3C",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L3C.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L3D",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L3D.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L3E",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Control diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L3E.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L4A",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L4A.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L4B",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L4B.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L4C",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L4C.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L4D",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L4D.d"}
},
{
"Subject ID":"-",
"Sample ID":"E_L4E",
"Factors":{"Genotype":"PHGDH+/-","Treatment":"Serine/glycine-depleted diet","Sample source":"Mouse back of eye"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"E_L4E.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Tissues were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80℃ until analysis","SAMPLE_TYPE":"Back of eye (choroid/RPE)","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":"Spectra 3µm C8SR column (3 μm particle, 3.0 × 150 mm; Peeke Scientific)","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% B; 27 min, 82% B; and 30 min, 82% B","FLOW_RATE":"0.5 mL/min","COLUMN_TEMPERATURE":"40°C"},

"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 metabolite metadata section."},

"MS_METABOLITE_DATA":{
"Units":"Normalized ion count/mg of protein",

"Data":[{"Metabolite":"Cer 18:1/16:0","E_L7A":"865.5163706","E_L7B":"1399.298202","E_L7C":"805.8821127","E_L7D":"733.9068606","E_L7E":"682.7560264","E_L8A":"675.5375613","E_L8B":"1010.272527","E_L8C":"783.7159583","E_L8D":"892.1641894","E_L8E":"778.7868466","E_L3A":"1020.73678","E_L3B":"890.4384282","E_L3C":"810.7402222","E_L3D":"953.3241564","E_L3E":"642.0182333","E_L4A":"782.8803563","E_L4B":"544.1971604","E_L4C":"774.5038775","E_L4D":"1167.15882","E_L4E":"644.7723089"},{"Metabolite":"Cer 18:1/18:0","E_L7A":"384.1812829","E_L7B":"375.6893528","E_L7C":"384.2376651","E_L7D":"380.9642481","E_L7E":"351.6998719","E_L8A":"352.9778456","E_L8B":"421.7293479","E_L8C":"366.6609662","E_L8D":"396.4480741","E_L8E":"393.1542287","E_L3A":"452.9283072","E_L3B":"473.3818215","E_L3C":"473.9498723","E_L3D":"451.3501583","E_L3E":"429.8576369","E_L4A":"406.2297477","E_L4B":"300.1439538","E_L4C":"334.3992029","E_L4D":"587.5147131","E_L4E":"347.4623945"},{"Metabolite":"Cer 18:1/20:0","E_L7A":"1053.116425","E_L7B":"1596.469854","E_L7C":"1220.974505","E_L7D":"922.7640187","E_L7E":"900.5562983","E_L8A":"1077.86675","E_L8B":"1342.671953","E_L8C":"947.5946757","E_L8D":"1187.156145","E_L8E":"998.818048","E_L3A":"1331.320859","E_L3B":"1208.009776","E_L3C":"1215.119264","E_L3D":"1376.534047","E_L3E":"1023.062571","E_L4A":"1011.542386","E_L4B":"1019.829296","E_L4C":"965.4711022","E_L4D":"1247.685636","E_L4E":"893.7909392"},{"Metabolite":"Cer 18:1/22:0","E_L7A":"901.4712851","E_L7B":"1404.938656","E_L7C":"897.0171311","E_L7D":"853.261433","E_L7E":"912.132819","E_L8A":"894.031562","E_L8B":"1197.037111","E_L8C":"826.0024055","E_L8D":"1036.893114","E_L8E":"903.2676536","E_L3A":"1086.758361","E_L3B":"1234.040097","E_L3C":"1133.067738","E_L3D":"1241.751952","E_L3E":"917.1915542","E_L4A":"775.5510121","E_L4B":"782.3775598","E_L4C":"791.8018256","E_L4D":"1192.11965","E_L4E":"776.1480869"},{"Metabolite":"Cer 18:1/24:0","E_L7A":"830.2337223","E_L7B":"1348.205916","E_L7C":"848.536063","E_L7D":"798.5247","E_L7E":"787.914812","E_L8A":"772.0529482","E_L8B":"1018.668166","E_L8C":"796.0272024","E_L8D":"909.5560224","E_L8E":"831.6233839","E_L3A":"943.8668121","E_L3B":"1076.986683","E_L3C":"993.4135836","E_L3D":"1083.889587","E_L3E":"838.0514788","E_L4A":"766.4062197","E_L4B":"869.2352918","E_L4C":"676.7954852","E_L4D":"964.0293049","E_L4E":"669.9894597"},{"Metabolite":"Cer 18:1/24:1","E_L7A":"642.5883471","E_L7B":"917.111886","E_L7C":"660.5424708","E_L7D":"547.3738963","E_L7E":"588.9797417","E_L8A":"588.032828","E_L8B":"716.0292191","E_L8C":"533.208904","E_L8D":"680.3943732","E_L8E":"588.6420063","E_L3A":"783.8040968","E_L3B":"772.6162222","E_L3C":"686.3854709","E_L3D":"787.0284625","E_L3E":"490.8726754","E_L4A":"627.8073073","E_L4B":"588.2160261","E_L4C":"499.8288346","E_L4D":"803.0501576","E_L4E":"473.7008018"},{"Metabolite":"DHCer 18:0/16:0","E_L7A":"12.6895934","E_L7B":"13.54496984","E_L7C":"11.71091193","E_L7D":"10.78027328","E_L7E":"10.01481485","E_L8A":"10.58057057","E_L8B":"15.12255536","E_L8C":"12.2121482","E_L8D":"13.10912892","E_L8E":"12.62441753","E_L3A":"13.37667057","E_L3B":"14.5255415","E_L3C":"13.1964872","E_L3D":"12.98701395","E_L3E":"10.74779202","E_L4A":"11.74963049","E_L4B":"7.598077948","E_L4C":"11.5353013","E_L4D":"16.21040726","E_L4E":"9.684019844"},{"Metabolite":"DHCer 18:0/18:0","E_L7A":"2.626307512","E_L7B":"3.059493868","E_L7C":"2.830996577","E_L7D":"3.570478965","E_L7E":"2.625104411","E_L8A":"2.65360865","E_L8B":"3.373782379","E_L8C":"2.861915688","E_L8D":"3.037074624","E_L8E":"3.25130725","E_L3A":"2.659108416","E_L3B":"3.241962284","E_L3C":"3.303116143","E_L3D":"3.571720422","E_L3E":"2.930395578","E_L4A":"3.071005614","E_L4B":"2.315597269","E_L4C":"2.658197069","E_L4D":"5.045115703","E_L4E":"2.465628123"},{"Metabolite":"DHCer 18:0/20:0","E_L7A":"3.49667775","E_L7B":"3.160058425","E_L7C":"2.835840095","E_L7D":"5.759603804","E_L7E":"3.111469056","E_L8A":"3.361134222","E_L8B":"3.84480465","E_L8C":"3.391137116","E_L8D":"3.918766243","E_L8E":"3.830434862","E_L3A":"3.447285996","E_L3B":"3.773919996","E_L3C":"3.885466712","E_L3D":"3.806208416","E_L3E":"3.400559068","E_L4A":"3.576598563","E_L4B":"2.733460314","E_L4C":"3.141567451","E_L4D":"5.386866562","E_L4E":"3.255316588"},{"Metabolite":"DHCer 18:0/22:0","E_L7A":"2.700347738","E_L7B":"2.350024023","E_L7C":"2.750086005","E_L7D":"2.082799337","E_L7E":"2.199840087","E_L8A":"3.196984153","E_L8B":"3.337154211","E_L8C":"3.17990632","E_L8D":"3.208323108","E_L8E":"3.338621085","E_L3A":"2.930323813","E_L3B":"2.928132964","E_L3C":"3.128188607","E_L3D":"3.658587169","E_L3E":"2.908752244","E_L4A":"3.051683591","E_L4B":"2.842361338","E_L4C":"2.905133822","E_L4D":"4.832267597","E_L4E":"2.930150749"},{"Metabolite":"DHCer 18:0/23:0","E_L7A":"0.327172976","E_L7B":"0.263619847","E_L7C":"0.368663182","E_L7D":"0.198612529","E_L7E":"0.225278862","E_L8A":"0.23737134","E_L8B":"0.348898817","E_L8C":"0.301478008","E_L8D":"0.36564753","E_L8E":"0.419722138","E_L3A":"0.186038919","E_L3B":"0.369025431","E_L3C":"0.695345192","E_L3D":"0.269913611","E_L3E":"0.242628959","E_L4A":"0.325254063","E_L4B":"0.241289409","E_L4C":"0.333908663","E_L4D":"0.479141419","E_L4E":"0.358641838"},{"Metabolite":"DHCer 18:0/24:0","E_L7A":"1.155045184","E_L7B":"1.372795871","E_L7C":"1.272416002","E_L7D":"1.243761108","E_L7E":"1.126318124","E_L8A":"1.921848324","E_L8B":"1.68117081","E_L8C":"1.440522087","E_L8D":"1.805497559","E_L8E":"1.661784962","E_L3A":"1.357847979","E_L3B":"1.855751369","E_L3C":"1.89496595","E_L3D":"1.681976981","E_L3E":"1.591144421","E_L4A":"1.663718235","E_L4B":"1.657672184","E_L4C":"1.313343849","E_L4D":"2.464449013","E_L4E":"1.363335946"},{"Metabolite":"DHCer 18:0/24:1","E_L7A":"1.463575574","E_L7B":"0.898114608","E_L7C":"1.225013047","E_L7D":"1.024808742","E_L7E":"0.810760111","E_L8A":"0.949808488","E_L8B":"1.717798977","E_L8C":"1.464800549","E_L8D":"1.388376971","E_L8E":"1.24642424","E_L3A":"1.489492019","E_L3B":"1.519013588","E_L3C":"1.031693618","E_L3D":"1.561164311","E_L3E":"0.86557362","E_L4A":"1.29356347","E_L4B":"1.00889657","E_L4C":"1.221007034","E_L4D":"2.340862799","E_L4E":"1.310533597"},{"Metabolite":"doxDHCer 18:0/18:0","E_L7A":"26.135295","E_L7B":"39.4068532","E_L7C":"27.78237228","E_L7D":"30.2867398","E_L7E":"22.86847882","E_L8A":"116.3031137","E_L8B":"79.5121148","E_L8C":"105.9052472","E_L8D":"112.2837191","E_L8E":"108.9410849","E_L3A":"27.98687673","E_L3B":"38.03112794","E_L3C":"30.58373218","E_L3D":"43.39186271","E_L3E":"30.91656924","E_L4A":"126.236977","E_L4B":"108.837257","E_L4C":"130.0378177","E_L4D":"120.5833209","E_L4E":"111.4016809"},{"Metabolite":"doxDHCer 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