#METABOLOMICS WORKBENCH STUDY_ID:ST000274 ANALYSIS_ID:AN000437 PROJECT_ID:PR000218 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE HIF 1 alpha PR:PROJECT_SUMMARY Glycolysis/TCA/Nucleotide analysis (AEC cells) PR:INSTITUTE University of Michigan PR:DEPARTMENT Surgery PR:LABORATORY Raghavendran Lab PR:LAST_NAME Raghavendran PR:FIRST_NAME Krishnan PR:ADDRESS Ann Arbor, MI PR:EMAIL kraghave@umich.edu PR:PHONE 734-615-7142 #STUDY ST:STUDY_TITLE HIF 1 alpha type 2 cells metabolomics ST:STUDY_TYPE Glycolysis/TCA/Nucleotide analysis (tissue/cells) ST:STUDY_SUMMARY Lung contusion is a major risk factor for the development of acute respiratory ST:STUDY_SUMMARY syndrome. Hypoxia-inducible factor-1? is the primary transcription factor that ST:STUDY_SUMMARY responsible for regulating the cellular response to changes in oxygen tension. ST:STUDY_SUMMARY set to determine if hypoxia-inducible factor-1? plays a role in the ST:STUDY_SUMMARY of acute inflammatory response and injury in lung contusion.Nonlethal ST:STUDY_SUMMARY unilateral lung contusion was induced in a hypoxia reporter mouse model and ST:STUDY_SUMMARY 2 cell-specific hypoxia-inducible factor-1? conditional knockout mice. The mice ST:STUDY_SUMMARY killed at 5-, 24-, 48-, and 72-hour time points, and the extent of systemic and ST:STUDY_SUMMARY hypoxia was assessed. In addition, injury and inflammation were assessed by ST:STUDY_SUMMARY bronchoalveolar lavage cells (flow cytometry and cytospin), albumin ST:STUDY_SUMMARY injury), and cytokines (inflammation). Isolated type 2 cells from the ST:STUDY_SUMMARY factor-1? conditional knockout mice were isolated and evaluated for ST:STUDY_SUMMARY cytokines following lung contusion. Finally, the role of nuclear factor-?B and ST:STUDY_SUMMARY as intermediates in this interaction was studied. ST:INSTITUTE University of Michigan ST:DEPARTMENT Surgery ST:LABORATORY Raghavendran Lab ST:LAST_NAME Thomas ST:FIRST_NAME Bivin ST:ADDRESS Ann Arbor, MI ST:EMAIL bthomas@umich.edu ST:PHONE 734-615-7142 ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 8 ST:STUDY_COMMENTS http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245055/ : HIF1 (+/+) stands for ST:STUDY_COMMENTS reporter mouse modelHIF1 (-/-) stands for type 2 cell-specific ST:STUDY_COMMENTS factor-1? conditional knockout #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:SPECIES_GROUP Mammal #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - S00014948 Genotype:HIF1 (-/-) | Treatment:Control SUBJECT_SAMPLE_FACTORS - S00014949 Genotype:HIF1 (-/-) | Treatment:Control SUBJECT_SAMPLE_FACTORS - S00014944 Genotype:HIF1 (+/+) | Treatment:Control SUBJECT_SAMPLE_FACTORS - S00014945 Genotype:HIF1 (+/+) | Treatment:Control SUBJECT_SAMPLE_FACTORS - S00014950 Genotype:HIF1 (-/-) | Treatment:Lung contusion, 24h SUBJECT_SAMPLE_FACTORS - S00014951 Genotype:HIF1 (-/-) | Treatment:Lung contusion, 24h SUBJECT_SAMPLE_FACTORS - S00014946 Genotype:HIF1 (+/+) | Treatment:Lung contusion, 24h SUBJECT_SAMPLE_FACTORS - S00014947 Genotype:HIF1 (+/+) | Treatment:Lung contusion, 24h SUBJECT_SAMPLE_FACTORS - S00020491 Genotype:Pooled sample | Treatment:Pooled cells #COLLECTION CO:COLLECTION_SUMMARY - CO:SAMPLE_TYPE Cells #TREATMENT TR:TREATMENT_SUMMARY - #SAMPLEPREP SP:SAMPLEPREP_SUMMARY - SP:SAMPLEPREP_PROTOCOL_FILENAME Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1260 CH:COLUMN_NAME Phenomenex Luna NH2 (150 x 1mm, 3um) CH:METHODS_ID AQM020 CH:METHODS_FILENAME QTOF-002-HILIC-35min-1mm-No_Insert.m #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME MRC2 (University of Michigan) AN:ACQUISITION_PARAMETERS_FILE QTOF-002-HILIC-35min-1mm-No_Insert.m AN:PROCESSING_PARAMETERS_FILE EX00307-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/µg protein MS_METABOLITE_DATA_START Samples S00014948 S00014949 S00014944 S00014945 S00014950 S00014951 S00014946 S00014947 Factors Genotype:HIF1 (-/-) | Treatment:Control Genotype:HIF1 (-/-) | Treatment:Control Genotype:HIF1 (+/+) | Treatment:Control Genotype:HIF1 (+/+) | Treatment:Control Genotype:HIF1 (-/-) | Treatment:Lung contusion, 24h Genotype:HIF1 (-/-) | Treatment:Lung contusion, 24h Genotype:HIF1 (+/+) | Treatment:Lung contusion, 24h Genotype:HIF1 (+/+) | Treatment:Lung contusion, 24h 2 or 3-phosphoglycerate_2PG/3PG 0.4923 0.7110 0.8611 2.2346 1.0397 0.6412 2.3720 1.7139 6-Phosphogluconate 0.2709 0.3188 0.3173 0.1616 0.0869 0.1352 0.2018 Acetyl-CoA 0.2649 0.2697 0.4070 0.7993 0.5029 0.2225 0.8440 0.5996 adenosine 1.8831 1.2545 10.3089 17.6305 38.8862 19.4795 7.2443 28.7146 ADP 11.5581 19.0367 10.9149 21.4723 4.7700 1.8193 37.5566 20.6323 AMP 398.5276 488.6746 1150.7201 1805.8813 1360.7255 892.2914 1090.6977 1167.0805 ATP 6.4894 10.4910 3.7231 7.8167 2.0310 0.8154 54.0677 16.8000 Citrate or Isocitrate 24.5583 34.5114 49.4800 78.4312 62.8255 44.1718 112.6494 93.5648 flavin adenine dinucleotide 0.2822 0.3058 0.4543 0.7097 0.6850 0.3389 0.8508 0.6878 Fructose 1_6-bisphosphate 9.8186 14.4112 13.1371 13.1023 11.0040 6.7597 33.2205 19.3991 Glucose 6-phosphate or fructose-6-phosphate 9.2556 10.2307 21.5468 27.8144 15.8916 11.5451 28.2213 24.5232 Lactate 26.6605 22.6068 26.6727 26.7212 35.9952 33.4328 47.9150 26.5791 Malate 88.9937 88.4946 109.7923 175.8938 132.4842 96.7829 215.3524 176.9606 Nicotinamide Adenine Dinucleotide oxidized 3.4073 4.3689 5.1978 9.8458 5.4708 2.6117 12.1045 8.8395 nicotinamide adenine dinucleotide phosphate oxidized 1.9389 2.6738 3.6820 6.0889 2.6102 1.2883 4.8533 3.8668 nicotinamide adenine dinucleotide phosphate reduced 2.0027 4.0838 23.8938 15.8830 Nicotinamide Adenine Dinucleotide reduced 0.1178 0.2256 Phosphoenolpyruvate 0.3793 Sucrose 210.2357 40.3946 62.2260 58.8831 82.2040 54.6808 101.3678 119.8509 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 2 or 3-phosphoglycerate_2PG/3PG 724 C00597 2PG/3PG UM_Target_ID 6-Phosphogluconate 91493 C00345 6PG UM_Target_ID Acetyl-CoA 444493 C00024 aCoA UM_Target_ID adenosine 60961 C00212 Adenosine UM_Target_ID ADP 6022 C00008 ADP UM_Target_ID AMP 6083 C00020 AMP UM_Target_ID ATP 5957 C00002 ATP UM_Target_ID Citrate or Isocitrate 311 C00158 CIT/ICIT UM_Target_ID flavin adenine dinucleotide 643975 C00016 FAD UM_Target_ID Fructose 1,6-bisphosphate 172313 C00354 FBP UM_Target_ID Glucose 6-phosphate or fructose-6-phosphate 5958 C00092 G6P/F6P UM_Target_ID Lactate 107689 C00186 LAC UM_Target_ID Malate 222656 C00149 MAL UM_Target_ID Nicotinamide Adenine Dinucleotide oxidized 10897651 C00003 NAD UM_Target_ID nicotinamide adenine dinucleotide phosphate oxidized 5886 C00006 NADP UM_Target_ID nicotinamide adenine dinucleotide phosphate reduced 5886 C00006 NADPH UM_Target_ID Nicotinamide Adenine Dinucleotide reduced 439153 C00004 NADH UM_Target_ID Phosphoenolpyruvate 1005 C00074 PEP UM_Target_ID Sucrose 5988 C00089 SUC UM_Target_ID METABOLITES_END #END