{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003272","ANALYSIS_ID":"AN005358","PROJECT_ID":"PR002030","VERSION":"1","CREATED_ON":"June 18, 2024, 10:03 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 for Biological Studies","DEPARTMENT":"Molecular and Cell Biology Laboratory","LABORATORY":"Metallo Lab","LAST_NAME":"Lim","FIRST_NAME":"Esther","ADDRESS":"10010 N Torrey Pines Rd, La Jolla, California, 92037, USA","EMAIL":"ewlim2024@gmail.com","PHONE":"(858) 453-4100","FUNDING_SOURCE":"R01CA234245"},
"STUDY":{"STUDY_TITLE":"Impact of serine supplementation following treatment with serine/glycine-depleted diet","STUDY_SUMMARY":"We analyzed metabolites in the retina, choroid/RPE, plasma, and paw skin from mice that were previously on control or serine/glycine-depleted diet and then switched over to a control or serine-supplemented diet.","INSTITUTE":"Salk Institute for Biological Studies","DEPARTMENT":"Molecular and Cell Biology Laboratory","LABORATORY":"Metallo Lab","LAST_NAME":"Lim","FIRST_NAME":"Esther","ADDRESS":"10010 N Torrey Pines Rd","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 months","WEIGHT_OR_WEIGHT_RANGE":"25-45 g","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"The Scripps Research Institute Vivarium","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":"LMRI_DietRev_BOE_20B2",
"Factors":{"Treatment":"Back of eye control","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20B2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20B3",
"Factors":{"Treatment":"Back of eye control","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20B3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20B4",
"Factors":{"Treatment":"Back of eye control","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20B4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20C2",
"Factors":{"Treatment":"Back of eye control","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20C2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20C3",
"Factors":{"Treatment":"Back of eye control","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20C3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20D1",
"Factors":{"Treatment":"Back of eye -SG diet","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20D1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20D2",
"Factors":{"Treatment":"Back of eye -SG diet","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20D2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20D3",
"Factors":{"Treatment":"Back of eye -SG diet","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20D3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20D4",
"Factors":{"Treatment":"Back of eye -SG diet","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20D4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20D5",
"Factors":{"Treatment":"Back of eye -SG diet","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20D5.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20H1",
"Factors":{"Treatment":"Back of eye High serine rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20H1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20H2",
"Factors":{"Treatment":"Back of eye High serine rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20H2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20H3",
"Factors":{"Treatment":"Back of eye High serine rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20H3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20H4",
"Factors":{"Treatment":"Back of eye High serine rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20H4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20H5",
"Factors":{"Treatment":"Back of eye High serine rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20H5.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20J1",
"Factors":{"Treatment":"Back of eye Control rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20J1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20J2",
"Factors":{"Treatment":"Back of eye Control rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20J2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20J3",
"Factors":{"Treatment":"Back of eye Control rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20J3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20J4",
"Factors":{"Treatment":"Back of eye Control rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20J4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_BOE_20J5",
"Factors":{"Treatment":"Back of eye Control rescue","Sample source":"Mouse back of eye (choroid/RPE)"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_BOE_20J5.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20B2",
"Factors":{"Treatment":"Retina control","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20B2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20B3",
"Factors":{"Treatment":"Retina control","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20B3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20B4",
"Factors":{"Treatment":"Retina control","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20B4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20C2",
"Factors":{"Treatment":"Retina control","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20C2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20C3",
"Factors":{"Treatment":"Retina control","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20C3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20D1",
"Factors":{"Treatment":"Retina -SG diet","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20D1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20D2",
"Factors":{"Treatment":"Retina -SG diet","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20D2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20D3",
"Factors":{"Treatment":"Retina -SG diet","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20D3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20D4",
"Factors":{"Treatment":"Retina -SG diet","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20D4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20D5",
"Factors":{"Treatment":"Retina -SG diet","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20D5.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20H1",
"Factors":{"Treatment":"Retina High serine rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20H1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20H2",
"Factors":{"Treatment":"Retina High serine rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20H2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20H3",
"Factors":{"Treatment":"Retina High serine rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20H3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20H4",
"Factors":{"Treatment":"Retina High serine rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20H4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20H5",
"Factors":{"Treatment":"Retina High serine rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20H5.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20J1",
"Factors":{"Treatment":"Retina Control rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20J1.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20J2",
"Factors":{"Treatment":"Retina Control rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20J2.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20J3",
"Factors":{"Treatment":"Retina Control rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20J3.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20J4",
"Factors":{"Treatment":"Retina Control rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20J4.d"}
},
{
"Subject ID":"-",
"Sample ID":"LMRI_DietRev_Retina_20J5",
"Factors":{"Treatment":"Retina Control rescue","Sample source":"Mouse Retina"},
"Additional sample data":{"RAW_FILE_NAME(Raw file name)":"LMRI_DietRev_Retina_20J5.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, back of the eye (choroid/RPE)"},
"TREATMENT":{"TREATMENT_SUMMARY":"Mice were fed control or serine/glycine-depleted (-SG) diet for 12 months. After 12 months, a subset of the mice that were on the -SG diet were switched back to either the control or supplemented diet for 4 months."},
"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%; 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 d18:1/14:0","LMRI_DietRev_BOE_20B2":"1.840154801","LMRI_DietRev_BOE_20B3":"2.126274725","LMRI_DietRev_BOE_20B4":"1.185622956","LMRI_DietRev_BOE_20C2":"2.724564944","LMRI_DietRev_BOE_20C3":"2.418660864","LMRI_DietRev_BOE_20D1":"2.028449416","LMRI_DietRev_BOE_20D2":"0.953769093","LMRI_DietRev_BOE_20D3":"1.489649482","LMRI_DietRev_BOE_20D4":"2.410806434","LMRI_DietRev_BOE_20D5":"","LMRI_DietRev_BOE_20H1":"2.241330018","LMRI_DietRev_BOE_20H2":"3.306692697","LMRI_DietRev_BOE_20H3":"3.249204218","LMRI_DietRev_BOE_20H4":"1.84839094","LMRI_DietRev_BOE_20H5":"1.165445174","LMRI_DietRev_BOE_20J1":"2.8294674","LMRI_DietRev_BOE_20J2":"1.867574121","LMRI_DietRev_BOE_20J3":"1.511682301","LMRI_DietRev_BOE_20J4":"2.633571116","LMRI_DietRev_BOE_20J5":"2.088732437","LMRI_DietRev_Retina_20B2":"1.245697473","LMRI_DietRev_Retina_20B3":"4.204085836","LMRI_DietRev_Retina_20B4":"1.426363226","LMRI_DietRev_Retina_20C2":"1.169405118","LMRI_DietRev_Retina_20C3":"1.018460314","LMRI_DietRev_Retina_20D1":"0.730644266","LMRI_DietRev_Retina_20D2":"0.572113922","LMRI_DietRev_Retina_20D3":"0.75691619","LMRI_DietRev_Retina_20D4":"1.700286637","LMRI_DietRev_Retina_20D5":"1.267682644","LMRI_DietRev_Retina_20H1":"1.016877479","LMRI_DietRev_Retina_20H2":"0.94258324","LMRI_DietRev_Retina_20H3":"0.900660987","LMRI_DietRev_Retina_20H4":"1.970797126","LMRI_DietRev_Retina_20H5":"0.881885698","LMRI_DietRev_Retina_20J1":"1.536448165","LMRI_DietRev_Retina_20J2":"1.043991352","LMRI_DietRev_Retina_20J3":"1.800398701","LMRI_DietRev_Retina_20J4":"0.792110899","LMRI_DietRev_Retina_20J5":"0.959703414"},{"Metabolite":"Cer 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}