{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000904","ANALYSIS_ID":"AN001471","VERSION":"1","CREATED_ON":"November 29, 2017, 3:23 pm"},

"PROJECT":{"PROJECT_TITLE":"Measurement of 2-hydroxyglutarate for reproducibility project","PROJECT_SUMMARY":"The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from IDH mutation impairs histone demethylation and results in a block to cell differentiation by Lu and colleagues, published in Nature in 2012 (Lu et al., 2012). The experiments that will be replicated are those reported in Figures 1B, 2A, 2B, 2D and 4D. Lu and colleagues demonstrated that expression of mutant forms of IDH1 or IDH2 caused global increases in histone methylation and increased levels of 2 hydroxyglutarate (Figure 1B). This was correlated with a block in differentiation (Figures 2A, B and D). This effect appeared to be mediated by the histone demethylase KDM4C (Figure 4D). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Scienceand Science Exchange, and the results of the replications will be published by eLife.","INSTITUTE":"Sanford Burnham Prebys Medical Discovery Institute","LAST_NAME":"Scott","FIRST_NAME":"David","ADDRESS":"10901 N. Torrey Pines Road, La Jolla, California, 92037, USA","EMAIL":"dscott@sbpdiscovery.org","PHONE":"858-646-3100"},

"STUDY":{"STUDY_TITLE":"Measurement of 2-hydroxyglutarate for reproducibility project","STUDY_SUMMARY":"Measurement of D-2-hydroxyglutarate and comparison of peak area with glutamate","INSTITUTE":"Sanford Burnham Prebys Medical Discovery Insititute","LAST_NAME":"David","FIRST_NAME":"Scott","ADDRESS":"10901 N. Torrey Pines Road","EMAIL":"dscott@sbpdiscovery.org","PHONE":"858-646-3100"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","CELL_STRAIN_DETAILS":"293T cells"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_vec2",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH1wt2",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH1mut2",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH2wt2",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run1_IDH2mut2",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH1wt2",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH1mut2",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH2wt2",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run2_IDH2mut2",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_vec2",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH1wt2",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH1mut2",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH2wt2",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run3_IDH2mut2",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run4_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run4_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run4_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run4_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run4_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run5_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run5_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run5_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run5_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run5_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run6_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run6_IDH1wt1",
"Factors":{"IDH expression":"IDH1wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run6_IDH1mut1",
"Factors":{"IDH expression":"IDH1mut"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run6_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"293T",
"Sample ID":"Prtcl1_Run6_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run1_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run1_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run1_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run2_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run2_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run2_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run3_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run3_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run3_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run4_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run4_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run4_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run5_vec1",
"Factors":{"IDH expression":"vector"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run5_IDH2wt1",
"Factors":{"IDH expression":"IDH2wt"}
},
{
"Subject ID":"3T3_L1",
"Sample ID":"Prtcl2_Run5_IDH2mut1",
"Factors":{"IDH expression":"IDH2mut"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were washed x3 in cold PBS, then scraped into 80% methanol containing 20 uM L-norvaline","COLLECTION_PROTOCOL_FILENAME":"GC-MS analysis of D-2-hydroxyglutarate","SAMPLE_TYPE":"Adherent cultured mammalian cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells transfected with empty vector or vector expressing wild-type or mutant isocitrate dehydrogenase (IDH1 or IDH2; mutations respectively R132H or R172K)"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Methanol/water extracts were counter-extracted with chloroform to remove non-polar metabolites, dried in a centrifugal evaporator, and derivatized in 60 ul 1:1 mix acetonitrile: MTBSTFA, with heating for 75 min at 75C"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Shimadzu","COLUMN_NAME":"Rxi-5ms"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Shimadzu QP2010 Plus","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"ion counts",

"Data":[{"Metabolite":"L-glutamic acid","Prtcl1_Run1_vec1":"1553494.595","Prtcl1_Run1_vec2":"1562635.135","Prtcl1_Run1_IDH1wt1":"2715159.459","Prtcl1_Run1_IDH1wt2":"2705972.973","Prtcl1_Run1_IDH1mut1":"3315413.514","Prtcl1_Run1_IDH1mut2":"3225586.486","Prtcl1_Run1_IDH2wt1":"4069710.811","Prtcl1_Run1_IDH2wt2":"3981932.432","Prtcl1_Run1_IDH2mut1":"3541029.73","Prtcl1_Run1_IDH2mut2":"3521472.973","Prtcl1_Run2_vec1":"32174445.95","Prtcl1_Run2_IDH1wt1":"33173521.62","Prtcl1_Run2_IDH1wt2":"37387854.05","Prtcl1_Run2_IDH1mut1":"669524.3243","Prtcl1_Run2_IDH1mut2":"4018556.757","Prtcl1_Run2_IDH2wt1":"33173521.62","Prtcl1_Run2_IDH2wt2":"34097886.49","Prtcl1_Run2_IDH2mut1":"415778.3784","Prtcl1_Run2_IDH2mut2":"1312451.351","Prtcl1_Run3_vec1":"4363089.189","Prtcl1_Run3_vec2":"4906618.919","Prtcl1_Run3_IDH1wt1":"12555597.3","Prtcl1_Run3_IDH1wt2":"12425705.41","Prtcl1_Run3_IDH1mut1":"3155270.27","Prtcl1_Run3_IDH1mut2":"3168751.351","Prtcl1_Run3_IDH2wt1":"18652443.24","Prtcl1_Run3_IDH2wt2":"18704972.97","Prtcl1_Run3_IDH2mut1":"1239713.514","Prtcl1_Run3_IDH2mut2":"1234521.622","Prtcl1_Run4_vec1":"63799932.43","Prtcl1_Run4_IDH1wt1":"51048481.08","Prtcl1_Run4_IDH1mut1":"35002643.24","Prtcl1_Run4_IDH2wt1":"81985983.78","Prtcl1_Run4_IDH2mut1":"7141408.108","Prtcl1_Run5_vec1":"181746421.6","Prtcl1_Run5_IDH1wt1":"120431208.1","Prtcl1_Run5_IDH1mut1":"22763681.08","Prtcl1_Run5_IDH2wt1":"141441454.1","Prtcl1_Run5_IDH2mut1":"14987764.86","Prtcl1_Run6_vec1":"150617324.3","Prtcl1_Run6_IDH1wt1":"115213051.4","Prtcl1_Run6_IDH1mut1":"35929856.76","Prtcl1_Run6_IDH2wt1":"136939213.5","Prtcl1_Run6_IDH2mut1":"15112213.51","Prtcl2_Run1_vec1":"189150462.2","Prtcl2_Run1_IDH2wt1":"80601170.27","Prtcl2_Run1_IDH2mut1":"2586600","Prtcl2_Run2_vec1":"123825802.7","Prtcl2_Run2_IDH2wt1":"88606029.73","Prtcl2_Run2_IDH2mut1":"1798159.459","Prtcl2_Run3_vec1":"182459118.9","Prtcl2_Run3_IDH2wt1":"163871129.7","Prtcl2_Run3_IDH2mut1":"7186083.784","Prtcl2_Run4_vec1":"82287772.97","Prtcl2_Run4_IDH2wt1":"51463489.19","Prtcl2_Run4_IDH2mut1":"14419786.49","Prtcl2_Run5_vec1":"191570345.9","Prtcl2_Run5_IDH2wt1":"82942559.46","Prtcl2_Run5_IDH2mut1":"13915467.57"},{"Metabolite":"D-2-hydroxyglutaric acid","Prtcl1_Run1_vec1":"4891","Prtcl1_Run1_vec2":"4030","Prtcl1_Run1_IDH1wt1":"31179","Prtcl1_Run1_IDH1wt2":"10930","Prtcl1_Run1_IDH1mut1":"116533","Prtcl1_Run1_IDH1mut2":"124929","Prtcl1_Run1_IDH2wt1":"49109","Prtcl1_Run1_IDH2wt2":"48235","Prtcl1_Run1_IDH2mut1":"4746244","Prtcl1_Run1_IDH2mut2":"4778555","Prtcl1_Run2_vec1":"53258","Prtcl1_Run2_IDH1wt1":"421863","Prtcl1_Run2_IDH1wt2":"160253","Prtcl1_Run2_IDH1mut1":"1076735","Prtcl1_Run2_IDH1mut2":"6474930","Prtcl1_Run2_IDH2wt1":"421863","Prtcl1_Run2_IDH2wt2":"458896","Prtcl1_Run2_IDH2mut1":"3988146","Prtcl1_Run2_IDH2mut2":"11779928","Prtcl1_Run3_vec1":"61647","Prtcl1_Run3_vec2":"32675","Prtcl1_Run3_IDH1wt1":"65606","Prtcl1_Run3_IDH1wt2":"85399","Prtcl1_Run3_IDH1mut1":"2143958","Prtcl1_Run3_IDH1mut2":"2103946","Prtcl1_Run3_IDH2wt1":"197851","Prtcl1_Run3_IDH2wt2":"192021","Prtcl1_Run3_IDH2mut1":"11387021","Prtcl1_Run3_IDH2mut2":"12590248","Prtcl1_Run4_vec1":"738822","Prtcl1_Run4_IDH1wt1":"193012","Prtcl1_Run4_IDH1mut1":"62542544","Prtcl1_Run4_IDH2wt1":"3574201","Prtcl1_Run4_IDH2mut1":"40399324","Prtcl1_Run5_vec1":"324505","Prtcl1_Run5_IDH1wt1":"674575","Prtcl1_Run5_IDH1mut1":"68545648","Prtcl1_Run5_IDH2wt1":"12152144","Prtcl1_Run5_IDH2mut1":"74409681","Prtcl1_Run6_vec1":"227722","Prtcl1_Run6_IDH1wt1":"1547759","Prtcl1_Run6_IDH1mut1":"56088853","Prtcl1_Run6_IDH2wt1":"3628324","Prtcl1_Run6_IDH2mut1":"72416259","Prtcl2_Run1_vec1":"1093230","Prtcl2_Run1_IDH2wt1":"469442","Prtcl2_Run1_IDH2mut1":"39431309","Prtcl2_Run2_vec1":"399407","Prtcl2_Run2_IDH2wt1":"569772","Prtcl2_Run2_IDH2mut1":"48555618","Prtcl2_Run3_vec1":"850754","Prtcl2_Run3_IDH2wt1":"893896","Prtcl2_Run3_IDH2mut1":"53355170","Prtcl2_Run4_vec1":"1228940","Prtcl2_Run4_IDH2wt1":"1115177","Prtcl2_Run4_IDH2mut1":"61027870","Prtcl2_Run5_vec1":"3380307","Prtcl2_Run5_IDH2wt1":"2380821","Prtcl2_Run5_IDH2mut1":"111581340"}],

"Metabolites":[{"Metabolite":"L-glutamic acid","retention index":"","quantified m/z":"432","PubChem ID":"33032","KEGG ID":""},{"Metabolite":"D-2-hydroxyglutaric acid","retention index":"","quantified m/z":"433","PubChem ID":"439391","KEGG ID":""}]
}

}