#METABOLOMICS WORKBENCH kenanazam_20160908_172222_mwtab.txt DATATRACK_ID:730 VERSION 1 CREATED_ON November 17, 2016, 3:26 pm #PROJECT PR:PROJECT_TITLE Effect of Odc knockout on amino acid homeostasis of Eu-Myc Lymphomas PR:PROJECT_TYPE Amino acid steady-state level analysis PR:PROJECT_SUMMARY Analysis of two B cell lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice PR:PROJECT_SUMMARY and two B cell lymphomas isolated from Eu-Myc;CD19-Cre;Odc +/+. CD19-Cre PR:PROJECT_SUMMARY expression leads to the deletion of Odc specifically in B cells. PR:INSTITUTE H. Lee Moffitt Cancer Center PR:DEPARTMENT Tumor Biology PR:LABORATORY John Cleveland PR:LAST_NAME Fernandez PR:FIRST_NAME Mario PR:ADDRESS 12902 Magnolia Drive, MRC 4-West PR:EMAIL mario.fernandez@moffitt.org PR:PHONE 813-745-5140 PR:FUNDING_SOURCE 5R01CA154739 #STUDY ST:STUDY_TITLE Effect of Odc knockout on amino acid homeostasis of Eu-Myc Lymphomas ST:STUDY_TYPE Lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice ST:STUDY_SUMMARY Amino acid levels analysis of lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl ST:STUDY_SUMMARY mic and their wild-type counterparts Eu-Myc;CD19-Cre;Odc +/+ ST:INSTITUTE University of Florida ST:DEPARTMENT SECIM ST:LABORATORY John Cleveland ST:LAST_NAME Fernandez ST:FIRST_NAME Mario ST:ADDRESS 12902 Magnolia Drive, MRC 4-West ST:EMAIL mario.fernandez@moffitt.org ST:PHONE 813-745-5140 ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 12 ST:STUDY_COMMENTS Lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice in triplicate #SUBJECT SU:SUBJECT_TYPE Cells SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:CELL_STRAIN_DETAILS BIT SU:SUBJECT_COMMENTS See study design section for cell number per sample SU:CELL_PRIMARY_IMMORTALIZED Immortalized #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS BIT636 BIT_001 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT636 BIT_002 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT636 BIT_003 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT642 BIT_004 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT642 BIT_005 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT642 BIT_006 Genotype:Odc +/+ SUBJECT_SAMPLE_FACTORS BIT654 BIT_007 Genotype:Odc -/- SUBJECT_SAMPLE_FACTORS BIT654 BIT_008 Genotype:Odc -/- SUBJECT_SAMPLE_FACTORS BIT654 BIT_009 Genotype:Odc -/- SUBJECT_SAMPLE_FACTORS BIT640 BIT_010 Genotype:Odc -/- SUBJECT_SAMPLE_FACTORS BIT640 BIT_011 Genotype:Odc -/- SUBJECT_SAMPLE_FACTORS BIT640 BIT_012 Genotype:Odc -/- #COLLECTION CO:COLLECTION_SUMMARY Cells were counted, cells were collected via centrifugation, washed twice with CO:COLLECTION_SUMMARY cold 1x PBS, PBS removed and flash frozen. Pellets were saved at -80 C. CO:SAMPLE_TYPE Cell CO:COLLECTION_METHOD Pellet CO:COLLECTION_LOCATION Lab CO:COLLECTION_TIME Collected during log phase CO:STORAGE_CONDITIONS Pellet at -80C CO:STORAGE_VIALS 1.5 mL microfuge tube CO:TISSUE_CELL_IDENTIFICATION BIT #TREATMENT TR:TREATMENT_SUMMARY Cells were not treated. Cells were collected during log phase TR:CELL_GROWTH_CONTAINER 6-well plate #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Amino acid SP:SAMPLEPREP_PROTOCOL_FILENAME SB_AA_Assay.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Amino Acid CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Waters AccQ Tag (100 x 2mm, 1.7um) CH:METHODS_FILENAME SB_AA_Assay.pdf #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME Sanford Burnham #MS MS:INSTRUMENT_NAME Agilent 6490 QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Amino Acids #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS nmol/mg protein MS_METABOLITE_DATA_START Samples BIT_001 BIT_002 BIT_003 BIT_004 BIT_005 BIT_006 BIT_007 BIT_008 BIT_009 BIT_010 BIT_011 BIT_012 Factors Genotype:Odc +/+ Genotype:Odc +/+ Genotype:Odc +/+ Genotype:Odc +/+ Genotype:Odc +/+ Genotype:Odc +/+ Genotype:Odc -/- Genotype:Odc -/- Genotype:Odc -/- Genotype:Odc -/- Genotype:Odc -/- Genotype:Odc -/- Alanine 0.92 0.80 2.45 0.88 1.01 1.01 1.47 1.27 1.53 6.52 5.78 5.64 Arginine 0.07 0.05 0.07 0.05 0.04 0.06 0.06 0.05 0.05 0.11 0.10 0.12 Asparagine 0.06 0.07 0.06 0.05 0.05 0.11 0.09 0.12 0.15 0.14 0.15 Aspartate 0.11 0.11 0.09 0.13 0.11 0.10 0.11 0.09 0.16 1.07 0.89 1.26 Glutamate 3.80 3.26 4.65 3.72 3.04 2.63 7.46 5.85 9.16 3.58 3.92 5.91 Glutamine 1.11 1.12 1.13 1.64 1.49 1.85 0.64 0.43 0.90 2.63 2.32 2.57 Glycine 0.88 1.01 1.22 1.30 1.30 1.37 3.59 3.31 2.76 1.33 1.58 1.53 Histidine 0.07 0.05 0.07 0.05 0.05 0.08 0.06 0.08 0.11 0.11 0.12 Isoleucine 0.13 0.13 0.21 0.11 0.11 0.12 0.14 0.14 0.15 0.20 0.23 0.27 Leucine 0.12 0.15 0.19 0.08 0.11 0.12 0.14 0.15 0.15 0.26 0.19 0.26 Phenylalanine 0.09 0.10 0.19 0.07 0.07 0.07 0.12 0.10 0.14 0.17 0.18 0.21 Proline 0.66 0.61 1.29 0.58 0.57 0.65 1.23 1.02 1.10 0.87 1.05 0.90 Serine 0.09 0.08 0.05 0.05 0.10 0.09 0.14 0.40 0.34 0.33 Threonine 0.46 0.30 0.85 0.51 0.63 0.54 0.51 0.53 0.62 1.37 1.24 1.16 Tryptophan 0.02 0.02 0.03 0.02 0.01 0.02 0.03 0.02 0.03 0.04 0.03 0.04 Tyrosine 0.10 0.08 0.16 0.08 0.09 0.09 0.17 0.11 0.13 0.20 0.20 0.19 Valine 0.17 0.14 0.25 0.13 0.12 0.12 0.21 0.15 0.20 0.26 0.27 0.31 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name retention index quantified m/z PubChem ID KEGG ID Alanine 4.16 260.17 5950 Arginine 2.68 345.21 6322 Asparagine 2.25 303.13 6267 Aspartate 2.99 304.11 5960 Glutamate 3.35 318.11 33032 Glutamine 2.65 317.21 5961 Glycine 2.81 246.08 750 Histidine 2.07 326.21 6274 Isoleucine 8.15 302.21 6306 Leucine 8.26 302.21 6106 Phenylalanine 8.40 336.21 6140 Proline 4.84 286.16 145742 Serine 2.60 276.11 5951 Threonine 3.74 290.11 6288 Tryptophan 8.54 375.21 6305 Tyrosine 6.66 352.21 6057 Valine 7.09 288.21 6287 METABOLITES_END #END