{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003084","ANALYSIS_ID":"AN005042","VERSION":"1","CREATED_ON":"02-16-2024"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics of Mouse Embryonic CSF Following Maternal Immune Activation","PROJECT_SUMMARY":"The embryonic cerebrospinal fluid (eCSF) is critical for the developing central nervous system (CNS), from neurogenesis to lifelong cognitive functions. Changes in eCSF composition due to inflammation can impact brain function. We recently identified an abnormal cytokine signature in eCSF following maternal immune activation (MIA), a mouse model of autism spectrum disorder (ASD). We hypothesized that MIA leads to other alterations in eCSF composition and employed untargeted metabolomics to profile changes in the eCSF metabolome in mice after inducing MIA with polyI:C. We report these data here as a resource, including a comprehensive MS1 and MS2 reference dataset, and present additional datasets comparing two mouse strains (CD-1 and C57Bl/6) and two developmental time points (E12.5 and E14.5). Targeted metabolomics further validated changes in eCSF upon MIA. We show a significant elevation of glucocorticoids and kynurenine pathway related metabolites. Both pathways are relevant for suppressing inflammation or could be informative as disease biomarkers. Our resource should inform future mechanistic studies regarding the etiology of MIA neuropathology and roles and contributions of eCSF metabolites to brain development.","INSTITUTE":"Boston Childrens Hospital","LAST_NAME":"Petrova","FIRST_NAME":"Boryana","ADDRESS":"300 Longwood Av, Boston, MA, 2115, USA","EMAIL":"boryana.petrova@childrens.harvard.edu","PHONE":"6173557433","DOI":"http://dx.doi.org/10.21228/M8ST6K"},

"STUDY":{"STUDY_TITLE":"Metabolome changes in embryonic CSF (Part 6)","STUDY_SUMMARY":"Untargeted MS analysis of embryonic CSF at E12.5, 2.5 hours after PolyI:C or saline injection into the mother.","INSTITUTE":"Boston Children's Hospital, Harvard Medical School","LABORATORY":"Kanarek Lab","LAST_NAME":"Petrova","FIRST_NAME":"Boryana","ADDRESS":"Enders 1116.2 300 Longwood Ave","EMAIL":"Boryana.Petrova@childrens.harvard.edu","PHONE":"6179197352","SUBMIT_DATE":"2024-01-16"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"10",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"PolyIC","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP968","Sample source information":"embryonic CSF 6"}
},
{
"Subject ID":"-",
"Sample ID":"8",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"PolyIC","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP964","Sample source information":"embryonic CSF 2"}
},
{
"Subject ID":"-",
"Sample ID":"9",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"PolyIC","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP966","Sample source information":"embryonic CSF 4"}
},
{
"Subject ID":"-",
"Sample ID":"4",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"saline","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP963","Sample source information":"embryonic CSF 1"}
},
{
"Subject ID":"-",
"Sample ID":"5",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"saline","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP965","Sample source information":"embryonic CSF 3"}
},
{
"Subject ID":"-",
"Sample ID":"6",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"saline","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP967","Sample source information":"embryonic CSF 5"}
},
{
"Subject ID":"-",
"Sample ID":"7",
"Factors":{"Sample source":"embryonic CSF","Developmental Timepoint":"E10-12.5","Maternal Treatment (injection)":"saline","Collection Timepoint":"2.5h"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP969","Sample source information":"embryonic CSF 7"}
},
{
"Subject ID":"-",
"Sample ID":"1",
"Factors":{"Sample source":"mock tube","Developmental Timepoint":"-","Maternal Treatment (injection)":"-","Collection Timepoint":"-"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP970","Sample source information":"mock tube"}
},
{
"Subject ID":"-",
"Sample ID":"2",
"Factors":{"Sample source":"mock tube","Developmental Timepoint":"-","Maternal Treatment (injection)":"-","Collection Timepoint":"-"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP971","Sample source information":"mock tube"}
},
{
"Subject ID":"-",
"Sample ID":"3",
"Factors":{"Sample source":"mock tube","Developmental Timepoint":"-","Maternal Treatment (injection)":"-","Collection Timepoint":"-"},
"Additional sample data":{"RAW_FILE_NAME":"20220303_QEF1_HILIC_eCSF_PolyIC2h5m_BP972","Sample source information":"mock tube"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"All animal studies were performed under the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital (BCH). All mice were housed in a 12h light-dark cycle with ad libitum access to food and water. CSF, eCSF, was collected from the cisterna magna of the pup embryos and mother, and centrifuged at 5,000g for 10 min. at 4 °C to remove any tissue debris. CSF samples were kept on ice and analyzed the same day as collection.","SAMPLE_TYPE":"Cerebrospinal fluid"},

"TREATMENT":{"TREATMENT_SUMMARY":"For polyI:C experiments: Pregnant female mice were injected intraperitoneally (route of administration) with a single dose of 20 mg/kg polyI:C (sigma aldrich) and controls will receive an injection of 0.9% saline embryonic day 12.5-14.5. Samples were collected either 3hrs or 48hrs post injection."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Per condition, 5uL of maternal serum, CSF, were extracted by brief sonication in 200/100μl (serum/csf) 80% methanol, supplemented with isotopically labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). 10uL Embryonic CSF (eCSF) was extracted per condition using the previously described buffer quantity, and the flash frozen liver chunks were extracted in 300uL of the previously described buffer. After centrifugation for 10min. at maximum speed on a benchtop centrifuge (Eppendorf) the cleared supernatant from CSF and eCSF was dried using a nitrogen dryer. Samples were reconstituted in LCMS water by brief sonication. Extracted metabolites were spun again and cleared supernatant was transferred in LC-MS microvials. Serum followed the same protocol, except that an additional 20-minute centrifugation was administered, and homogenization for 5 minutes. Final LCMS water reconstitution values for tissue type were 50uL (maternal and embryonic serum), 15uL (maternal CSF and eCSF),. A small amount of each sample was pooled and serially diluted 3 and 10-fold to be used as quality controls throughout the batch run. Two microliters (equivalent to 0.2 ul of CSF) of reconstituted sample were injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore) operated on a Dionex UltiMate 3000 UPLC system (Thermo Fisher Scientific). Chromatographic separation was achieved using the following conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, 0.1% ammonium hydroxide. Gradient conditions were: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B. The column oven and autosampler tray were held at 25 °C and 4 °C, respectively. The MS data acquisition was on a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe and was performed in a range of m/z= 70–1000, with the resolution set at 70,000, the AGC target at 1x106, and the maximum injection time (Max IT) at 20 msec. For tSIM scans, the resolution was set at 70,000, the AGC target was 1x105, and the max IT was 100 msec. Relative quantitation of polar metabolites was performed with TraceFinder 4.1 (Thermo Fisher Scientific) using a 5 ppm mass tolerance and referencing an in-house library of chemical standards. Pooled samples and fractional dilutions were prepared as quality controls and only those metabolites were taken for further analysis, for which the correlation between the dilution factor and the peak area was >0.95 (high confidence metabolites)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"ZIC-pHILIC","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)","COLUMN_TEMPERATURE":"25","FLOW_GRADIENT":"0-20 min: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B.","FLOW_RATE":"0.150mL/minute","SOLVENT_A":"100% acetonitrile","SOLVENT_B":"100% water; 20mM ammonium carbonate, 0.1% ammonium hydroxide","CHROMATOGRAPHY_TYPE":"HILIC"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"BCH_Kanarek_Lab_protocol.pdf"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"HESI, See uploaded BCH_Kanarek_Lab_protocol.pdf for metabolite metadata Tags key and explanation","ION_MODE":"POSITIVE","MS_RESULTS_FILE":"ST003084_AN005042_Results.txt UNITS:a.u. Has m/z:Yes Has RT:Yes RT units:Minutes"},

"MS_METABOLITE_DATA":{
"Units":"a.u.",

"Data":[{"Metabolite":"1_4-Dimethylimidazole","10":"58880792.7100","8":"61655927.6300","9":"49945420.1300","4":"39435154.7400","5":"59222651.9400","6":"70730502.4000","7":"60170849.3000","1":"4272603.0420","2":"17350198.8500","3":"3097935.4070"},{"Metabolite":"1-[(9Z)-hexadecenoyl]-sn-glycero-3-phosphocholine","10":"41777786.0500","8":"59817186.0100","9":"52800428.5100","4":"40433541.1700","5":"48399759.8100","6":"44192992.0800","7":"33356953.3100","1":"1015809.4180","2":"1025084.8230","3":"804614.0492"},{"Metabolite":"(.+/-.)-1-Amino-2-propanol","10":"181134036.6000","8":"506475389.7000","9":"645680887.2000","4":"567278989.8000","5":"238320883.8000","6":"511153638.3000","7":"500806214.7000","1":"567975.9381","2":"1123364.1820","3":"786583.9606"},{"Metabolite":"1-(beta-D-Ribofuranosyl)-1_3_4_7-tetrahydro-2H-1_3-diazepin-2-one","10":"69266014.3700","8":"66150929.2900","9":"69428469.8300","4":"55117471.0000","5":"68298813.1700","6":"76888070.8400","7":"77458690.9200","1":"13962799.7300","2":"13174472.5700","3":"6248788.0010"},{"Metabolite":"1-Methylguanine","10":"149403901.6000","8":"145736626.4000","9":"138458465.6000","4":"135519587.5000","5":"125421591.0000","6":"150636653.7000","7":"135788639.7000","1":"894392.6023","2":"1132333.9540","3":"1039718.8220"},{"Metabolite":"1-METHYL-L-HISTIDINE","10":"1330030643.0000","8":"1161998439.0000","9":"1159365476.0000","4":"1268196380.0000","5":"1197255628.0000","6":"1061555337.0000","7":"1348419609.0000","1":"37753556.6400","2":"18475328.8700","3":"16365707.7400"},{"Metabolite":"1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine","10":"671775.6221","8":"1358889.1280","9":"635718.1562","4":"325554.7103","5":"995232.9778","6":"1084724.4400","7":"920492.4215","1":"76677.4853","2":"106410.0153","3":"40984.0099"},{"Metabolite":"1-(sn-glycero-3-phospho)-1D-myo-inositol","10":"13100572.0100","8":"12842713.5000","9":"13443210.3500","4":"11500459.7600","5":"13047739.8400","6":"14254931.1800","7":"15040417.3200","1":"189685.1228","2":"206180.1715","3":"172439.1660"},{"Metabolite":"2-[(2Z)-2-({4-[(3-Aminopropyl)amino]butyl}imino)-2-hydroxyethyl]-2-hydroxysuccinic acid (1)","10":"47332827.1000","8":"37318569.3700","9":"42234613.7400","4":"33156054.3900","5":"38927488.0800","6":"43335841.5000","7":"37744332.9200","1":"574210.5681","2":"678427.8877","3":"606208.5459"},{"Metabolite":"2-[(2Z)-2-({4-[(3-Aminopropyl)amino]butyl}imino)-2-hydroxyethyl]-2-hydroxysuccinic acid (2)","10":"3134446.5220","8":"2486328.0510","9":"2691713.5670","4":"2568237.3980","5":"1935830.5040","6":"3167282.9900","7":"3240055.0280","1":"195197.7035","2":"208594.1242","3":"174290.2988"},{"Metabolite":"2_3_6-Pyridinetriol","10":"19958582.5900","8":"11854417.4600","9":"14270930.5300","4":"14367414.3900","5":"16439770.2700","6":"20044926.0400","7":"18389473.9400","1":"3941747.7460","2":"4928816.7310","3":"2960845.9270"},{"Metabolite":"2_4-Diacetamido-2_4_6-trideoxy-alpha-D-mannopyranose (RT = 6.642)","10":"86100526.1400","8":"74686777.4400","9":"87178224.7300","4":"82132756.9100","5":"73279124.2900","6":"105419199.7000","7":"87906114.1000","1":"9994605.9960","2":"67944145.8200","3":"15705414.7800"},{"Metabolite":"2_4-Diacetamido-2_4_6-trideoxy-alpha-D-mannopyranose (RT = 8.138)","10":"199508476.3000","8":"234353626.9000","9":"259825707.0000","4":"199313275.5000","5":"218808400.8000","6":"225123853.5000","7":"246145735.4000","1":"1384161.4790","2":"2162043.2280","3":"603732.7432"},{"Metabolite":"2_4-Diamino-6-nitrotoluene (1)","10":"123971011.5000","8":"94655617.9900","9":"135045169.3000","4":"126788616.0000","5":"138345633.7000","6":"94890857.3700","7":"162999543.5000","1":"7186393.9460","2":"10377837.1300","3":"1392842.6970"},{"Metabolite":"2_4-Diamino-6-nitrotoluene (2)","10":"61453990.4500","8":"59849897.2400","9":"69682022.6800","4":"86872634.1500","5":"71600298.7900","6":"57770373.0800","7":"111901711.8000","1":"12206900.2900","2":"15103088.0600","3":"1109111.4670"},{"Metabolite":"2_6-Diamino-4-methyleneheptanedioic acid","10":"504300872.1000","8":"224510241.3000","9":"452224874.9000","4":"281582516.3000","5":"531591911.8000","6":"534327815.5000","7":"505211559.8000","1":"24165852.9000","2":"341706164.3000","3":"86302490.5900"},{"Metabolite":"2_6-Diamino-7-hydroxynonanedioic acid","10":"14974185.2100","8":"6882461.7390","9":"8213604.5690","4":"6721299.6190","5":"9459608.1830","6":"13375853.4000","7":"8947770.8740","1":"264963.8381","2":"962645.6651","3":"236302.2891"},{"Metabolite":"2-Amino-4-methylpyrimidine","10":"182687029.7000","8":"127396613.8000","9":"151882632.3000","4":"184918861.3000","5":"141263556.2000","6":"116671447.7000","7":"182638904.7000","1":"25484255.3700","2":"5962660.5500","3":"307591.7386"},{"Metabolite":"2-formylphenylformamide","10":"212191961.3000","8":"196652299.9000","9":"221180734.6000","4":"221592317.2000","5":"218393780.0000","6":"190612340.2000","7":"190149452.6000","1":"10836168.1700","2":"6049626.5010","3":"6967307.2830"},{"Metabolite":"2-Hydroxycinnamic acid","10":"241092156.7000","8":"145258823.5000","9":"143360270.9000","4":"187552964.7000","5":"177370293.3000","6":"136409891.7000","7":"183115891.1000","1":"360688.5963","2":"466896.1224","3":"736666.6745"},{"Metabolite":"(2R)-3-{[(2-Aminoethoxy)(hydroxy)phosphoryl]oxy}-2-{[10-(2-hexylcyclopropyl)decanoyl]oxy}propyl palmitate","10":"79092528.7000","8":"111095328.0000","9":"87404491.7300","4":"36453409.0000","5":"77506643.8800","6":"89453663.0800","7":"63594130.4900","1":"176800.5396","2":"235797.7751","3":"101874.6983"},{"Metabolite":"(2S)-2-Amino-8-hydroxyoctanoic acid","10":"13083994.1000","8":"13618059.2100","9":"16950462.2600","4":"10104671.3600","5":"16022335.1800","6":"28122935.1300","7":"13893187.4000","1":"592523.2874","2":"567456.0839","3":"545555.7230"},{"Metabolite":"3-[(1S_4R)-4-Hydroxy-2-cyclohexen-1-yl]-L-alanine","10":"32694902.5700","8":"32095424.1900","9":"32249364.0900","4":"27624871.3600","5":"33817321.2800","6":"36997542.8200","7":"38574698.9800","1":"503899.7319","2":"742452.3345","3":"599445.7888"},{"Metabolite":"3-Buten-1-amine","10":"301233534.7000","8":"317028866.3000","9":"338156096.2000","4":"325275203.5000","5":"343914951.4000","6":"297586307.2000","7":"359024914.7000","1":"3070324.2660","2":"805455.7217","3":"9633053.6500"},{"Metabolite":"3-METHYL-L-HISTIDINE","10":"684399122.3000","8":"553742586.9000","9":"610900093.4000","4":"634239747.1000","5":"751427588.4000","6":"529453939.9000","7":"736290718.6000","1":"37369183.8300","2":"24216409.5700","3":"16365707.7400"},{"Metabolite":"3-Morpholinopropanal","10":"12801288.4000","8":"10882354.1100","9":"11348373.9400","4":"13315154.3900","5":"13679378.5100","6":"13999464.9600","7":"15144439.1200","1":"1575906.3880","2":"1651195.4220","3":"209411.2013"},{"Metabolite":"3-Thiomorpholinecarboxylic acid","10":"34752950.2600","8":"28827382.1000","9":"35300926.9800","4":"33714133.8500","5":"64478443.1800","6":"46513370.8800","7":"38754808.4200","1":"325094.5043","2":"333237.8402","3":"315459.8163"},{"Metabolite":"3-ureidopropionate","10":"95182601.5800","8":"156515169.2000","9":"150715201.3000","4":"153227669.5000","5":"107988692.3000","6":"144104222.6000","7":"128496840.9000","1":"1190132.1640","2":"446313.0976","3":"412060.6142"},{"Metabolite":"4-Hydroxybenzaldehyde","10":"51631705.5100","8":"32798877.9500","9":"31894300.7600","4":"41580868.5400","5":"42495903.2500","6":"28408906.5100","7":"41271613.1500","1":"377204.5561","2":"1769604.0090","3":"2740535.9070"},{"Metabolite":"4-Hydroxyphenylacetylglycine","10":"12840684.7600","8":"7966840.2500","9":"10189138.3400","4":"9300018.0390","5":"10260331.8900","6":"14176171.7300","7":"15777050.3600","1":"205693.1130","2":"201847.5249","3":"180206.6084"},{"Metabolite":"4-Imidazolemethanol","10":"105902890.6000","8":"100708504.5000","9":"103828195.1000","4":"99666792.6400","5":"97311203.9700","6":"106689140.9000","7":"97251278.0900","1":"7262249.9740","2":"68914115.8300","3":"23823682.8000"},{"Metabolite":"4-Methyleneglutamine","10":"404536925.2000","8":"351885585.0000","9":"366288150.4000","4":"463541970.6000","5":"487167750.4000","6":"470190530.9000","7":"423694253.7000","1":"34104969.5800","2":"36897133.3300","3":"29112776.5200"},{"Metabolite":"4-(Methylthio)-2-oxobutyric acid","10":"213975059.1000","8":"130181034.9000","9":"160817112.4000","4":"168705899.4000","5":"193139484.5000","6":"211809770.5000","7":"179247796.6000","1":"744356.3916","2":"795225.1661","3":"764534.3010"},{"Metabolite":"5-Acetamidopentanoic acid (1)","10":"46625237.8400","8":"44474454.3300","9":"45151465.5500","4":"40664132.3100","5":"44009230.3000","6":"47981920.0500","7":"57137735.2500","1":"1515684.2540","2":"2635229.3630","3":"722120.5987"},{"Metabolite":"5-Acetamidopentanoic acid (2)","10":"40931311.0200","8":"38213889.8900","9":"35467263.9800","4":"31256223.1800","5":"38836244.1700","6":"41975657.5400","7":"43819953.8600","1":"1443820.9920","2":"2635229.3630","3":"1394767.6630"},{"Metabolite":"5-Hydroxyindole-3-acetic 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