#METABOLOMICS WORKBENCH araskind_20150610_9735441_mwtab.txt DATATRACK_ID:300 STUDY_ID:ST000199 ANALYSIS_ID:AN000301 PROJECT_ID:PR000154 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE IDH1 and Glioma PR:PROJECT_SUMMARY IDH1 is overexpresed in gliomas and knockdown of IDH1 leads to increased PR:PROJECT_SUMMARY therapy-induced cell death PR:INSTITUTE Northwestern University PR:DEPARTMENT Neurology PR:LABORATORY Stegh Lab PR:LAST_NAME Stegh PR:FIRST_NAME Alexander PR:ADDRESS Evanston, IL PR:EMAIL a-stegh@northwestern.edu PR:PHONE 312-503-2879 #STUDY ST:STUDY_TITLE IDH1 and Glioma knockdown idh1 (part II) ST:STUDY_SUMMARY Tumor neurospheres were grown in culture until 90% confluent. To collect cells, ST:STUDY_SUMMARY were filtered through 0.45um nylon filters (Fischer Sci 099029) that were ST:STUDY_SUMMARY with methanol and ultrapure water using a microanalytical glass filter holder ST:STUDY_SUMMARY Sci 09753E). The cells were filtered through filtration apparatus, then washed ST:STUDY_SUMMARY 1mL of distilled water very quickly. Filter paper is taken immediatedly with ST:STUDY_SUMMARY and plunged cell side down into 6-well plate filled with liquid nitrogen placed ST:STUDY_SUMMARY dry ice. Plate is wrapped in aluminum foil and stored at -80C before the liquid ST:STUDY_SUMMARY evaporates. Samples are shipped on dry ice ST:INSTITUTE University of Michigan ST:DEPARTMENT Biomedical Research Core Facilities ST:LABORATORY Metabolomics core ST:LAST_NAME Kachman ST:FIRST_NAME Maureen ST:ADDRESS 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 ST:EMAIL mkachman@umich.edu ST:PHONE - ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 10 #SUBJECT SU:SUBJECT_TYPE - SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS SU0004254 S00014999 Knockdown of IDH1:n/a SUBJECT_SAMPLE_FACTORS SU0004254 S00015000 Knockdown of IDH1:n/a SUBJECT_SAMPLE_FACTORS SU0004254 S00015001 Knockdown of IDH1:n/a SUBJECT_SAMPLE_FACTORS SU0004254 S00015002 Knockdown of IDH1:n/a SUBJECT_SAMPLE_FACTORS SU0004254 S00015003 Knockdown of IDH1:n/a SUBJECT_SAMPLE_FACTORS SU0004254 S00015004 Knockdown of IDH1:yes SUBJECT_SAMPLE_FACTORS SU0004254 S00015005 Knockdown of IDH1:yes SUBJECT_SAMPLE_FACTORS SU0004254 S00015006 Knockdown of IDH1:yes SUBJECT_SAMPLE_FACTORS SU0004254 S00015007 Knockdown of IDH1:yes SUBJECT_SAMPLE_FACTORS SU0004254 S00015008 Knockdown of IDH1:yes #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Cells, Cultured #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME Acyl-carnitines_analysis_protocol-CR-MK-20150528.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1200 CH:COLUMN_NAME Waters Acquity HSS T3 (50 x 2.1mm, 1.8um) CH:METHODS_ID AQM050 CH:METHODS_FILENAME QM-004-Xbridg2mm_ACar+_MRM-Insert.m.zip #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ACQUISITION_PARAMETERS_FILE QM-004-Xbridg2mm_ACar+_MRM-Insert.m.zip AN:PROCESSING_PARAMETERS_FILE EX00311-acyl-carnitines-quant.m.zip #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6490 QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00014999 S00015000 S00015001 S00015002 S00015003 S00015004 S00015005 S00015006 S00015007 S00015008 Factors Knockdown of IDH1:n/a Knockdown of IDH1:n/a Knockdown of IDH1:n/a Knockdown of IDH1:n/a Knockdown of IDH1:n/a Knockdown of IDH1:yes Knockdown of IDH1:yes Knockdown of IDH1:yes Knockdown of IDH1:yes Knockdown of IDH1:yes 3-hydroxylauroylcarnitine 0.0008 0.0007 0.0013 0.0008 0.0001 0.0011 0.0010 0.0030 0.0024 0.0022 3-Hydroxylinoleoylcarnitine 0.1148 0.0852 0.1639 0.0799 0.0826 0.1672 0.0939 0.2873 0.1910 0.1956 3-hydroxymyristoylcarnitine 0.0060 0.0050 0.0056 0.0027 0.0034 0.0084 0.0049 0.0138 0.0095 0.0078 3-Hydroxypalmitoylcarnitine 0.0146 0.0090 0.0134 0.0069 0.0084 0.0133 0.0066 0.0216 0.0126 0.0135 Acetylcarnitine 19.8971 16.4317 22.5422 16.5401 12.9806 81.2444 44.0475 79.8879 64.3582 61.5523 arachidonoylcarnitine 0.0018 0.0008 0.0020 0.0024 0.0010 0.0203 0.0012 0.0026 0.0039 0.0021 butyrylcarnitine 0.3544 0.2994 0.4361 0.2922 0.2454 0.6995 0.3850 0.7448 0.5552 0.5307 Decanoylcarnitine 0.0072 0.0087 0.0119 0.0072 0.0081 0.0103 0.0062 0.0139 0.0099 0.0138 decenoylcarnitine 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Dodecenoylcarnitine 0.0073 0.0059 0.0100 0.0050 0.0058 0.0103 0.0073 0.0116 0.0101 0.0121 Glutarylcarnitine 0.0038 0.0016 0.0016 0.0035 0.0013 0.0053 0.0017 0.0071 0.0049 0.0047 Hexanoylcarnitine 0.0027 0.0044 0.0064 0.0030 0.0034 0.0145 0.0033 0.0237 0.0128 0.0164 icosadienoylcarnitine 0.0007 0.0001 0.0005 0.0001 0.0000 0.0003 0.0003 0.0004 0.0004 0.0001 Icosanoylcarnitine 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 icosatrienoylcarnitine 0.0650 0.0699 0.0743 0.0361 0.0618 0.1061 0.0891 0.4644 0.1931 0.2635 icoseneoylcarnitine 0.0098 0.0085 0.0081 0.0045 0.0069 0.0169 0.0127 0.0627 0.0261 0.0347 isovalerylcarnitine 0.2867 0.2230 0.3100 0.2204 0.1707 0.1962 0.1227 0.2027 0.1892 0.1721 lauroylcarnitine 0.0000 0.0008 0.0002 0.0001 0.0003 0.0009 0.0001 0.0001 0.0005 0.0005 L-Carnitine 34.2595 25.9039 34.0476 21.3902 23.9979 37.5044 21.0793 44.7552 34.0823 35.5254 Linoelaidyl carnitine 0.0015 0.0018 0.0022 0.0012 0.0010 0.0040 0.0028 0.0085 0.0039 0.0057 myristoylcarnitine 0.0059 0.0073 0.0051 0.0027 0.0115 0.0061 0.0084 0.0141 0.0059 0.0102 octanoylcarnitine 0.0033 0.0042 0.0075 0.0025 0.0035 0.0055 0.0043 0.0111 0.0056 0.0093 Octenoylcarnitine 0.0000 0.0007 0.0005 0.0005 0.0009 0.0002 0.0005 0.0015 0.0003 0.0009 Oleoylcarnitine 0.0003 0.0002 0.0002 0.0000 0.0002 0.0002 0.0003 0.0000 0.0003 0.0000 Palmitoleylcarnitine 0.0255 0.0221 0.0379 0.0189 0.0199 0.0431 0.0241 0.0835 0.0564 0.0606 palmitoylcarnitine 0.0140 0.0202 0.0119 0.0087 0.0241 0.0133 0.0182 0.0298 0.0121 0.0158 propionylcarnitine 2.3420 1.8883 2.5318 1.9318 1.4225 3.3553 1.8524 3.0057 2.5391 2.3110 Stearoylcarnitine 0.0019 0.0003 0.0005 0.0011 0.0003 0.0023 0.0012 0.0039 0.0033 0.0027 Tetradecadiencarnitine 0.0005 0.0004 0.0007 0.0002 0.0004 0.0014 0.0005 0.0012 0.0002 0.0004 Tetradecenoylcarnitine 0.0127 0.0129 0.0114 0.0070 0.0102 0.0201 0.0109 0.0294 0.0171 0.0209 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type 3-hydroxylauroylcarnitine 71464535 C12-OH UM_Target_ID 3-Hydroxylinoleoylcarnitine 78076335 C18:2-OH UM_Target_ID 3-hydroxymyristoylcarnitine 71464541 C14-OH UM_Target_ID 3-Hydroxypalmitoylcarnitine 71464553 C16-OH UM_Target_ID Acetylcarnitine 1 C2 UM_Target_ID arachidonoylcarnitine 71464486 C20:4 UM_Target_ID butyrylcarnitine 439829 C4 UM_Target_ID Decanoylcarnitine 3332882 C10:0 UM_Target_ID decenoylcarnitine 54074509 C10:1 UM_Target_ID Dodecenoylcarnitine 53481671 C12:1 UM_Target_ID Glutarylcarnitine 71317118 C5:0-DC UM_Target_ID Hexanoylcarnitine 6426853 C6:0 UM_Target_ID icosadienoylcarnitine 163425699 C20:2 UM_Target_ID Icosanoylcarnitine 53477833 C20 UM_Target_ID icosatrienoylcarnitine C20:3 UM_Target_ID icoseneoylcarnitine 71464507 C20:1 UM_Target_ID isovalerylcarnitine 6426852 C5:0 UM_Target_ID lauroylcarnitine 168381 C12:0 UM_Target_ID L-Carnitine 10917 L-Carnitine UM_Target_ID Linoelaidyl carnitine 53477834 C18:2 UM_Target_ID myristoylcarnitine 3413344 C14:0 UM_Target_ID octanoylcarnitine 123701 C8:0 UM_Target_ID Octenoylcarnitine 71464472 C8:1 UM_Target_ID Oleoylcarnitine 166952 C18:1 UM_Target_ID Palmitoleylcarnitine 76040365 C16:1 UM_Target_ID palmitoylcarnitine 461 C16:0 UM_Target_ID propionylcarnitine 107738 C3 UM_Target_ID Stearoylcarnitine 5282 C18:0 UM_Target_ID Tetradecadiencarnitine 53481681 C14:2 UM_Target_ID Tetradecenoylcarnitine 22833575 C14:1 UM_Target_ID METABOLITES_END #END