#METABOLOMICS WORKBENCH Marcella_20210831_060903_mwtab.txt DATATRACK_ID:2817 STUDY_ID:ST001941 ANALYSIS_ID:AN003159 PROJECT_ID:PR001229 VERSION 1 CREATED_ON September 6, 2021, 12:55 am #PROJECT PR:PROJECT_TITLE Untargeted metabolomics of breast cell lines in the presence or the absence of PR:PROJECT_TITLE CtBP inhibitors PR:PROJECT_SUMMARY Experiments to test the effect of CtBP2 inhibition on metabolism of breast cell PR:PROJECT_SUMMARY lines PR:INSTITUTE University of Milano-Bicocca PR:LAST_NAME Bonanomi PR:FIRST_NAME Marcella PR:ADDRESS Piazza della Scienza 4, Milan, MI, 20126, Italy PR:EMAIL marcella.bonanomi@unimib.it PR:PHONE +390264483343 #STUDY ST:STUDY_TITLE Untargeted metabolomics of breast cell lines in the presence or the absence of ST:STUDY_TITLE CtBP inhibitors ST:STUDY_SUMMARY Experiments to test the effect of CtBP2 inhibition on metabolism of breast cell ST:STUDY_SUMMARY lines. In particular, experiment 1 involves comparison between a normal breast ST:STUDY_SUMMARY cell line (MCF102A) and a triple-negative breast cancer cell line (MDA-MB231). ST:STUDY_SUMMARY Experiment 2 is a study between MDA-MB231 silenced for CtBP2 by stable RNA ST:STUDY_SUMMARY interference (shCtBP2 cells) compared to scramble (shCTRL cells). Experiment 3 ST:STUDY_SUMMARY is a comparison between a normal breast cell line (MCF102A) and a ST:STUDY_SUMMARY triple-negative breast cancer cell line (MDA-MB231)in the presence of the ST:STUDY_SUMMARY absence of small-molecule CtBP inhibitors: HIPP (400 μM) or P4 (300 μM)for 48 ST:STUDY_SUMMARY hours. ST:INSTITUTE University of Milano-Bicocca ST:LAST_NAME Bonanomi ST:FIRST_NAME Marcella ST:ADDRESS Piazza della Scienza 4 ST:EMAIL marcella.bonanomi@unimib.it ST:PHONE +390264483343 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_001.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_002.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_003.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_001.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_002.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_003.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_001.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_002.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_003.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_001.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_002.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_003.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=1 SUBJECT_SAMPLE_FACTORS - sh CTRL_001.mzdata CELL LINE:MDA-MB231 | TREATMENT:SCRAMBLE EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - sh CTRL_002.mzdata CELL LINE:MDA-MB231 | TREATMENT:SCRAMBLE EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - sh CTRL_003.mzdata CELL LINE:MDA-MB231 | TREATMENT:SCRAMBLE EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - shCtBP2_001.mzdata CELL LINE:MDA-MB231 | TREATMENT:shCtBP2 EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - shCtBP2_002.mzdata CELL LINE:MDA-MB231 | TREATMENT:shCtBP2 EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - shCtBP2_003.mzdata CELL LINE:MDA-MB231 | TREATMENT:shCtBP2 EXPERIMENT=2 SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_1.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_2.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A CTRL 1_3.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_1.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_2.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A CTRL 2_3.mzdata CELL LINE:MCF102A | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 1_1.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 1_2.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 1_3.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 2_1.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 2_2.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A HIPP 2_3.mzdata CELL LINE:MCF102A | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 1_1.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 1_2.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 1_3.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 2_1.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 2_2.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 10A P4 2_3.mzdata CELL LINE:MCF102A | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 1_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 CTRL 2_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:CONTROL EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 1_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 1_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 1_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 2_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 2_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 HIPP 2_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:HIPP EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 1_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 1_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 1_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 2_1.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 2_2.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 SUBJECT_SAMPLE_FACTORS - 231 P4 2_3.mzdata CELL LINE:MDA-MB231 | TREATMENT:P4 EXPERIMENT=3 #COLLECTION CO:COLLECTION_SUMMARY MDA-MB231 and MCF102A cell lines were obtained from the American Type Culture CO:COLLECTION_SUMMARY Collection (ATCC) (LGC Standard, UK). MDA-MB231 cell line was grown in CO:COLLECTION_SUMMARY Dulbecco's modified Eagle's medium (DMEM) containing 4mM L-glutamine, CO:COLLECTION_SUMMARY supplemented with 10% fetal bovine serum. MCF102A cell line was maintained in CO:COLLECTION_SUMMARY DMEM/F-12 containing 5% horse serum, 2.5mM L-glutamine, 20ng/ml EGF, 100 ng/ml CO:COLLECTION_SUMMARY cholera toxin, 0.01 mg/ml insulin, and 500 ng/ml hydrocortisone. All media were CO:COLLECTION_SUMMARY supplemented with 100 U/ml penicillin and 100 µg/ml streptomycin, and cells CO:COLLECTION_SUMMARY were incubated at 37°C in a 5% CO2 incubator. CO:SAMPLE_TYPE Breast cancer cells #TREATMENT TR:TREATMENT_SUMMARY cells were plated in 6-well plates with normal growth medium and then incubated TR:TREATMENT_SUMMARY for 48h in a complete fresh medium in the presence or absence of treatments TR:TREATMENT_SUMMARY (HIPP 400 μM or P4 300 μM) #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Cells were quickly rinsed with NaCl 0.9% and quenched with 500μl ice-cold 70:30 SP:SAMPLEPREP_SUMMARY acetonitrile: water. Plates were placed at -80°C for 10 minutes, collected by SP:SAMPLEPREP_SUMMARY scraping, sonicated 5 sec for five pulses at 70% power twice, and then SP:SAMPLEPREP_SUMMARY centrifuged at 12000g for 10 min at 4°C. The supernatant was collected in a SP:SAMPLEPREP_SUMMARY glass insert and evaporated under airflow at 37°C. Samples were then SP:SAMPLEPREP_SUMMARY resuspended with 150 μl of H2O before analyses. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Agilent InfintyLab Poroshell 120 PFP column (2.1 x 100 mm, 2.7 μm) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6550 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS - MS:MS_RESULTS_FILE ST001941_AN003159_Results.txt UNITS:Area Has m/z:Neutral masses Has RT:Yes RT units:Minutes #END