#METABOLOMICS WORKBENCH gauravsarode143_20221222_103958 DATATRACK_ID:3666 STUDY_ID:ST002424 ANALYSIS_ID:AN003947 PROJECT_ID:PR001560 VERSION 1 CREATED_ON December 28, 2022, 8:52 am #PROJECT PR:PROJECT_TITLE Part2 : Integrated gut microbiome and lipidomic analyses in animal models of PR:PROJECT_TITLE Wilson disease reveal a role of intestine ATP7B in copper-related metabolic PR:PROJECT_TITLE dysregulation PR:PROJECT_SUMMARY Although the main pathogenic mechanism of Wilson disease (WD) is related to PR:PROJECT_SUMMARY copper accumulation in the liver and brain, there is limited knowledge about the PR:PROJECT_SUMMARY role of ATP7B copper transporter in extra-hepatic organs, including the PR:PROJECT_SUMMARY intestine, and how it could affect metabolic manifestations of the disease. The PR:PROJECT_SUMMARY aims of the present study were to profile and correlate the gut microbiota and PR:PROJECT_SUMMARY lipidome in mouse models of WD, and to study the metabolic effects of PR:PROJECT_SUMMARY intestine-specific ATP7B deficiency in a newly generated mouse model. Animal PR:PROJECT_SUMMARY models of WD presented reduced gut microbiota diversity compared to mice with PR:PROJECT_SUMMARY normal copper metabolism. Comparative prediction analysis of the functional PR:PROJECT_SUMMARY metagenome showed the involvement of several pathways including amino acid, PR:PROJECT_SUMMARY carbohydrate, and lipid metabolisms. Lipidomic profiles showed dysregulated tri- PR:PROJECT_SUMMARY and diglyceride, phospholipid, and sphingolipid metabolism. When challenged with PR:PROJECT_SUMMARY a high-fat diet, Atp7bΔIEC mice confirmed profound deregulation of fatty acid PR:PROJECT_SUMMARY desaturation and sphingolipid metabolism pathways as well as altered APOB48 PR:PROJECT_SUMMARY distribution in intestinal epithelial cells. Gut microbiome and lipidomic PR:PROJECT_SUMMARY analyses reveal integrated metabolic changes underlying the systemic PR:PROJECT_SUMMARY manifestations of WD. Intestine-specific ATP7B deficit affects both intestine PR:PROJECT_SUMMARY and systemic response to high-fat challenge. WD is as systemic disease and PR:PROJECT_SUMMARY organ-specific ATP7B variants can explain the varied phenotypic presentations. PR:INSTITUTE University of California, Davis PR:DEPARTMENT Department of Internal Medicine, Division of Hepatology/Gastroenterology PR:LAST_NAME Sarode PR:FIRST_NAME Gaurav Vilas PR:ADDRESS 451 E. Health Sciences Dr. Genome and Biomedical Sciences Facility Room 6404A PR:ADDRESS Davis, CA 95616 PR:EMAIL gsarode@ucdavis.edu PR:PHONE 5307526715 PR:FUNDING_SOURCE National Institutes of Health grants R01DK104770 (V.M.) #STUDY ST:STUDY_TITLE Integrated gut microbiome and lipidomic analyses in animal models of Wilson ST:STUDY_TITLE disease reveal a role of intestine ATP7B in copper-related metabolic ST:STUDY_TITLE dysregulation ST:STUDY_SUMMARY Although the main pathogenic mechanism of Wilson disease (WD) is related to ST:STUDY_SUMMARY copper accumulation in the liver and brain, there is limited knowledge about the ST:STUDY_SUMMARY role of ATP7B copper transporter in extra-hepatic organs, including the ST:STUDY_SUMMARY intestine, and how it could affect metabolic manifestations of the disease. The ST:STUDY_SUMMARY aims of the present study were to profile and correlate the gut microbiota and ST:STUDY_SUMMARY lipidome in mouse models of WD, and to study the metabolic effects of ST:STUDY_SUMMARY intestine-specific ATP7B deficiency in a newly generated mouse model. Animal ST:STUDY_SUMMARY models of WD presented reduced gut microbiota diversity compared to mice with ST:STUDY_SUMMARY normal copper metabolism. Comparative prediction analysis of the functional ST:STUDY_SUMMARY metagenome showed the involvement of several pathways including amino acid, ST:STUDY_SUMMARY carbohydrate, and lipid metabolisms. Lipidomic profiles showed dysregulated tri- ST:STUDY_SUMMARY and diglyceride, phospholipid, and sphingolipid metabolism. When challenged with ST:STUDY_SUMMARY a high-fat diet, Atp7bΔIEC mice confirmed profound deregulation of fatty acid ST:STUDY_SUMMARY desaturation and sphingolipid metabolism pathways as well as altered APOB48 ST:STUDY_SUMMARY distribution in intestinal epithelial cells. Gut microbiome and lipidomic ST:STUDY_SUMMARY analyses reveal integrated metabolic changes underlying the systemic ST:STUDY_SUMMARY manifestations of WD. Intestine-specific ATP7B deficit affects both intestine ST:STUDY_SUMMARY and systemic response to high-fat challenge. WD is as systemic disease and ST:STUDY_SUMMARY organ-specific ATP7B variants can explain the varied phenotypic presentations. ST:INSTITUTE University of California, Davis ST:DEPARTMENT Internal Medicine ST:LABORATORY Medici's Lab ST:LAST_NAME Sarode ST:FIRST_NAME Gaurav Vilas ST:ADDRESS 451 E. Health Sciences Dr. Genome and Biomedical Sciences Facility Room 6404A ST:ADDRESS Davis, CA 95616 ST:EMAIL gsarode@ucdavis.edu ST:PHONE 5307526715 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #FACTORS #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 iKO-IEC9-1 ShibataLiver024_MX562952_posCSH_iKO-IEC9-1-001.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver024_MX562952_posCSH_iKO-IEC9-1-001.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-2 ShibataLiver010_MX562952_posCSH_iKO-IEC9-2-002.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver010_MX562952_posCSH_iKO-IEC9-2-002.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-3 ShibataLiver026_MX562952_posCSH_iKO-IEC9-3-003.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver026_MX562952_posCSH_iKO-IEC9-3-003.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-4 ShibataLiver005_MX562952_posCSH_iKO-IEC9-4-004.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver005_MX562952_posCSH_iKO-IEC9-4-004.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-5 ShibataLiver006_MX562952_posCSH_iKO-IEC9-5-005.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver006_MX562952_posCSH_iKO-IEC9-5-005.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-6 ShibataLiver028_MX562952_posCSH_iKO-IEC9-6-006.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver028_MX562952_posCSH_iKO-IEC9-6-006.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-7 ShibataLiver012_MX562952_posCSH_iKO-IEC9-7-007.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver012_MX562952_posCSH_iKO-IEC9-7-007.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-8 ShibataLiver016_MX562952_posCSH_iKO-IEC9-8-008.d Treatment:iKO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver016_MX562952_posCSH_iKO-IEC9-8-008.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-1 ShibataLiver018_MX562952_posCSH_iWT-IEC9-1-009.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver018_MX562952_posCSH_iWT-IEC9-1-009.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-2 ShibataLiver022_MX562952_posCSH_iWT-IEC9-2-010.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver022_MX562952_posCSH_iWT-IEC9-2-010.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-3 ShibataLiver013_MX562952_posCSH_iWT-IEC9-3-011.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver013_MX562952_posCSH_iWT-IEC9-3-011.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-4 ShibataLiver033_MX562952_posCSH_iWT-IEC9-4-012.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver033_MX562952_posCSH_iWT-IEC9-4-012.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-5 ShibataLiver011_MX562952_posCSH_iWT-IEC9-5-013.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver011_MX562952_posCSH_iWT-IEC9-5-013.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-6 ShibataLiver029_MX562952_posCSH_iWT-IEC9-6-014.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver029_MX562952_posCSH_iWT-IEC9-6-014.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-7 ShibataLiver032_MX562952_posCSH_iWT-IEC9-7-015.d Treatment:iWT 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver032_MX562952_posCSH_iWT-IEC9-7-015.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-1 ShibataLiver002_MX562952_posCSH_iKO-IEChf9-1-016.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver002_MX562952_posCSH_iKO-IEChf9-1-016.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-2 ShibataLiver020_MX562952_posCSH_iKO-IEChf9-2-017.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver020_MX562952_posCSH_iKO-IEChf9-2-017.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-3 ShibataLiver001_MX562952_posCSH_iKO-IEChf9-3-018.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver001_MX562952_posCSH_iKO-IEChf9-3-018.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-4 ShibataLiver023_MX562952_posCSH_iKO-IEChf9-4-019.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver023_MX562952_posCSH_iKO-IEChf9-4-019.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-5 ShibataLiver004_MX562952_posCSH_iKO-IEChf9-5-020.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver004_MX562952_posCSH_iKO-IEChf9-5-020.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-6 ShibataLiver021_MX562952_posCSH_iKO-IEChf9-6-021.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver021_MX562952_posCSH_iKO-IEChf9-6-021.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-7 ShibataLiver031_MX562952_posCSH_iKO-IEChf9-7-022.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver031_MX562952_posCSH_iKO-IEChf9-7-022.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-8 ShibataLiver017_MX562952_posCSH_iKO-IEChf9-8-023.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver017_MX562952_posCSH_iKO-IEChf9-8-023.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-1 ShibataLiver007_MX562952_posCSH_KO-IEChf9-1-024.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver007_MX562952_posCSH_KO-IEChf9-1-024.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-2 ShibataLiver030_MX562952_posCSH_KO-IEChf9-2-025.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver030_MX562952_posCSH_KO-IEChf9-2-025.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-3 ShibataLiver025_MX562952_posCSH_KO-IEChf9-3-026.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver025_MX562952_posCSH_KO-IEChf9-3-026.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-4 ShibataLiver015_MX562952_posCSH_KO-IEChf9-4-027.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver015_MX562952_posCSH_KO-IEChf9-4-027.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-1 ShibataLiver027_MX562952_posCSH_WT-IEChf9-1-028.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver027_MX562952_posCSH_WT-IEChf9-1-028.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-2 ShibataLiver014_MX562952_posCSH_WT-IEChf9-2-029.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver014_MX562952_posCSH_WT-IEChf9-2-029.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-3 ShibataLiver019_MX562952_posCSH_WT-IEChf9-3-030.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver019_MX562952_posCSH_WT-IEChf9-3-030.d SUBJECT_SAMPLE_FACTORS KO-IEC9-1 ShibataLiver009_MX562952_posCSH_KO-IEC9-1-031.d Treatment:KO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver009_MX562952_posCSH_KO-IEC9-1-031.d SUBJECT_SAMPLE_FACTORS KO-IEC9-2 ShibataLiver003_MX562952_posCSH_KO-IEC9-2-032.d Treatment:KO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver003_MX562952_posCSH_KO-IEC9-2-032.d SUBJECT_SAMPLE_FACTORS KO-IEC9-3 ShibataLiver008_MX562952_posCSH_KO-IEC9-3-033.d Treatment:KO 5001 Species=Mouse; Organ=Liver; RAW_FILE_NAME=ShibataLiver008_MX562952_posCSH_KO-IEC9-3-033.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-1 ShibataPlasma024_MX562952_posCSH_iKO-IEC9-1-034.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma024_MX562952_posCSH_iKO-IEC9-1-034.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-2 ShibataPlasma010_MX562952_posCSH_iKO-IEC9-2-035.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma010_MX562952_posCSH_iKO-IEC9-2-035.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-3 ShibataPlasma026_MX562952_posCSH_iKO-IEC9-3-036.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma026_MX562952_posCSH_iKO-IEC9-3-036.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-4 ShibataPlasma005_MX562952_posCSH_iKO-IEC9-4-037.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma005_MX562952_posCSH_iKO-IEC9-4-037.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-5 ShibataPlasma006_MX562952_posCSH_iKO-IEC9-5-038_2.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma006_MX562952_posCSH_iKO-IEC9-5-038_2.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-6 ShibataPlasma028_MX562952_posCSH_iKO-IEC9-6-039.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma028_MX562952_posCSH_iKO-IEC9-6-039.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-7 ShibataPlasma012_MX562952_posCSH_iKO-IEC9-7-040.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma012_MX562952_posCSH_iKO-IEC9-7-040.d SUBJECT_SAMPLE_FACTORS iKO-IEC9-8 ShibataPlasma016_MX562952_posCSH_iKO-IEC9-8-041.d Treatment:iKO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma016_MX562952_posCSH_iKO-IEC9-8-041.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-1 ShibataPlasma018_MX562952_posCSH_iWT-IEC9-1-042.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma018_MX562952_posCSH_iWT-IEC9-1-042.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-2 ShibataPlasma022_MX562952_posCSH_iWT-IEC9-2-043.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma022_MX562952_posCSH_iWT-IEC9-2-043.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-3 ShibataPlasma013_MX562952_posCSH_iWT-IEC9-3-044.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma013_MX562952_posCSH_iWT-IEC9-3-044.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-4 ShibataPlasma033_MX562952_posCSH_iWT-IEC9-4-045.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma033_MX562952_posCSH_iWT-IEC9-4-045.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-5 ShibataPlasma011_MX562952_posCSH_iWT-IEC9-5-046.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma011_MX562952_posCSH_iWT-IEC9-5-046.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-6 ShibataPlasma029_MX562952_posCSH_iWT-IEC9-6-047.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma029_MX562952_posCSH_iWT-IEC9-6-047.d SUBJECT_SAMPLE_FACTORS iWT-IEC9-7 ShibataPlasma032_MX562952_posCSH_iWT-IEC9-7-048.d Treatment:iWT 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma032_MX562952_posCSH_iWT-IEC9-7-048.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-1 ShibataPlasma002_MX562952_posCSH_iKO-IEChf9-1-049.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma002_MX562952_posCSH_iKO-IEChf9-1-049.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-2 ShibataPlasma020_MX562952_posCSH_iKO-IEChf9-2-050.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma020_MX562952_posCSH_iKO-IEChf9-2-050.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-3 ShibataPlasma001_MX562952_posCSH_iKO-IEChf9-3-051.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma001_MX562952_posCSH_iKO-IEChf9-3-051.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-4 ShibataPlasma023_MX562952_posCSH_iKO-IEChf9-4-052.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma023_MX562952_posCSH_iKO-IEChf9-4-052.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-5 ShibataPlasma004_MX562952_posCSH_iKO-IEChf9-5-053.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma004_MX562952_posCSH_iKO-IEChf9-5-053.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-6 ShibataPlasma021_MX562952_posCSH_iKO-IEChf9-6-054.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma021_MX562952_posCSH_iKO-IEChf9-6-054.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-7 ShibataPlasma031_MX562952_posCSH_iKO-IEChf9-7-055.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma031_MX562952_posCSH_iKO-IEChf9-7-055.d SUBJECT_SAMPLE_FACTORS iKO-IEChf9-8 ShibataPlasma017_MX562952_posCSH_iKO-IEChf9-8-056.d Treatment:iKO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma017_MX562952_posCSH_iKO-IEChf9-8-056.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-1 ShibataPlasma007_MX562952_posCSH_KO-IEChf9-1-057.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma007_MX562952_posCSH_KO-IEChf9-1-057.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-2 ShibataPlasma030_MX562952_posCSH_KO-IEChf9-2-058.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma030_MX562952_posCSH_KO-IEChf9-2-058.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-3 ShibataPlasma025_MX562952_posCSH_KO-IEChf9-3-059.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma025_MX562952_posCSH_KO-IEChf9-3-059.d SUBJECT_SAMPLE_FACTORS KO-IEChf9-4 ShibataPlasma015_MX562952_posCSH_KO-IEChf9-4-060.d Treatment:KO 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma015_MX562952_posCSH_KO-IEChf9-4-060.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-1 ShibataPlasma027_MX562952_posCSH_WT-IEChf9-1-061.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma027_MX562952_posCSH_WT-IEChf9-1-061.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-2 ShibataPlasma014_MX562952_posCSH_WT-IEChf9-2-062.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma014_MX562952_posCSH_WT-IEChf9-2-062.d SUBJECT_SAMPLE_FACTORS WT-IEChf9-3 ShibataPlasma019_MX562952_posCSH_WT-IEChf9-3-063.d Treatment:WT 60% kcal fat Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma019_MX562952_posCSH_WT-IEChf9-3-063.d SUBJECT_SAMPLE_FACTORS KO-IEC9-1 ShibataPlasma009_MX562952_posCSH_KO-IEC9-1-064.d Treatment:KO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma009_MX562952_posCSH_KO-IEC9-1-064.d SUBJECT_SAMPLE_FACTORS KO-IEC9-2 ShibataPlasma003_MX562952_posCSH_KO-IEC9-2-065.d Treatment:KO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma003_MX562952_posCSH_KO-IEC9-2-065.d SUBJECT_SAMPLE_FACTORS KO-IEC9-3 ShibataPlasma008_MX562952_posCSH_KO-IEC9-3-066.d Treatment:KO 5001 Species=Mouse; Organ=Plasma; RAW_FILE_NAME=ShibataPlasma008_MX562952_posCSH_KO-IEC9-3-066.d SUBJECT_SAMPLE_FACTORS BiorecLiver001 BiorecLiver001_MX562952_posCSH_preShibataLiver001.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=BiorecLiver001_MX562952_posCSH_preShibataLiver001.d SUBJECT_SAMPLE_FACTORS BiorecLiver002 BiorecLiver002_MX562952_posCSH_postShibataLiver010.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=BiorecLiver002_MX562952_posCSH_postShibataLiver010.d SUBJECT_SAMPLE_FACTORS BiorecLiver003 BiorecLiver003_MX562952_posCSH_postShibataLiver020.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=BiorecLiver003_MX562952_posCSH_postShibataLiver020.d SUBJECT_SAMPLE_FACTORS BiorecLiver004 BiorecLiver004_MX562952_posCSH_postShibataLiver030.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=BiorecLiver004_MX562952_posCSH_postShibataLiver030.d SUBJECT_SAMPLE_FACTORS BiorecLiver005 BiorecLiver005_MX562952_posCSH_postShibataLiver033.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=BiorecLiver005_MX562952_posCSH_postShibataLiver033.d SUBJECT_SAMPLE_FACTORS BiorecPlasma001 BiorecPlasma001_MX562952_posCSH_preShibataPlasma001.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=BiorecPlasma001_MX562952_posCSH_preShibataPlasma001.d SUBJECT_SAMPLE_FACTORS BiorecPlasma002 BiorecPlasma002_MX562952_posCSH_postShibataPlasma010.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=BiorecPlasma002_MX562952_posCSH_postShibataPlasma010.d SUBJECT_SAMPLE_FACTORS BiorecPlasma003 BiorecPlasma003_MX562952_posCSH_postShibataPlasma020.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=BiorecPlasma003_MX562952_posCSH_postShibataPlasma020.d SUBJECT_SAMPLE_FACTORS BiorecPlasma004 BiorecPlasma004_MX562952_posCSH_postShibataPlasma030.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=BiorecPlasma004_MX562952_posCSH_postShibataPlasma030.d SUBJECT_SAMPLE_FACTORS BiorecPlasma005 BiorecPlasma005_MX562952_posCSH_postShibataPlasma033.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=BiorecPlasma005_MX562952_posCSH_postShibataPlasma033.d SUBJECT_SAMPLE_FACTORS MtdBlank001 MtdBlank001_MX562952_posCSH_preShibataLiver001.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank001_MX562952_posCSH_preShibataLiver001.d SUBJECT_SAMPLE_FACTORS MtdBlank001 MtdBlank001_MX562952_posCSH_preShibataPlasma001.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank001_MX562952_posCSH_preShibataPlasma001.d SUBJECT_SAMPLE_FACTORS MtdBlank002 MtdBlank002_MX562952_posCSH_postShibataLiver010.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank002_MX562952_posCSH_postShibataLiver010.d SUBJECT_SAMPLE_FACTORS MtdBlank002 MtdBlank002_MX562952_posCSH_postShibataPlasma010.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank002_MX562952_posCSH_postShibataPlasma010.d SUBJECT_SAMPLE_FACTORS MtdBlank003 MtdBlank003_MX562952_posCSH_postShibataLiver020.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank003_MX562952_posCSH_postShibataLiver020.d SUBJECT_SAMPLE_FACTORS MtdBlank003 MtdBlank003_MX562952_posCSH_postShibataPlasma020.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank003_MX562952_posCSH_postShibataPlasma020.d SUBJECT_SAMPLE_FACTORS MtdBlank004 MtdBlank004_MX562952_posCSH_postShibataLiver030.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank004_MX562952_posCSH_postShibataLiver030.d SUBJECT_SAMPLE_FACTORS MtdBlank004 MtdBlank004_MX562952_posCSH_postShibataPlasma030.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank004_MX562952_posCSH_postShibataPlasma030.d SUBJECT_SAMPLE_FACTORS MtdBlank005 MtdBlank005_MX562952_posCSH_postShibataLiver033.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank005_MX562952_posCSH_postShibataLiver033.d SUBJECT_SAMPLE_FACTORS MtdBlank005 MtdBlank005_MX562952_posCSH_postShibataPlasma033.d Treatment:- Species=-; Organ=-; RAW_FILE_NAME=MtdBlank005_MX562952_posCSH_postShibataPlasma033.d SUBJECT_SAMPLE_FACTORS PoolQC001 PoolQC001_MX562952_posCSH_preShibataLiver001.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=PoolQC001_MX562952_posCSH_preShibataLiver001.d SUBJECT_SAMPLE_FACTORS PoolQC001 PoolQC001_MX562952_posCSH_preShibataPlasma001.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=PoolQC001_MX562952_posCSH_preShibataPlasma001.d SUBJECT_SAMPLE_FACTORS PoolQC002 PoolQC002_MX562952_posCSH_postShibataLiver010.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=PoolQC002_MX562952_posCSH_postShibataLiver010.d SUBJECT_SAMPLE_FACTORS PoolQC002 PoolQC002_MX562952_posCSH_postShibataPlasma010.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=PoolQC002_MX562952_posCSH_postShibataPlasma010.d SUBJECT_SAMPLE_FACTORS PoolQC003 PoolQC003_MX562952_posCSH_postShibataLiver020.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=PoolQC003_MX562952_posCSH_postShibataLiver020.d SUBJECT_SAMPLE_FACTORS PoolQC003 PoolQC003_MX562952_posCSH_postShibataPlasma020.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=PoolQC003_MX562952_posCSH_postShibataPlasma020.d SUBJECT_SAMPLE_FACTORS PoolQC004 PoolQC004_MX562952_posCSH_postShibataLiver030.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=PoolQC004_MX562952_posCSH_postShibataLiver030.d SUBJECT_SAMPLE_FACTORS PoolQC004 PoolQC004_MX562952_posCSH_postShibataPlasma030.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=PoolQC004_MX562952_posCSH_postShibataPlasma030.d SUBJECT_SAMPLE_FACTORS PoolQC005 PoolQC005_MX562952_posCSH_postShibataLiver033.d Treatment:- Species=Mouse; Organ=Liver; RAW_FILE_NAME=PoolQC005_MX562952_posCSH_postShibataLiver033.d SUBJECT_SAMPLE_FACTORS PoolQC005 PoolQC005_MX562952_posCSH_postShibataPlasma033.d Treatment:- Species=Mouse; Organ=Plasma; RAW_FILE_NAME=PoolQC005_MX562952_posCSH_postShibataPlasma033.d #COLLECTION CO:COLLECTION_SUMMARY The liver was isolated. Blood samples were centrifuged at 8,000 rpm for 10 CO:COLLECTION_SUMMARY minutes and the plasma was aliquoted. All samples were stored at -80°C until CO:COLLECTION_SUMMARY further analysis. CO:SAMPLE_TYPE Liver CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY From 8 weeks of age, tx-j, KO, and Atp7bΔIEC mice, and their respective TR:TREATMENT_SUMMARY controls, were either continued on LabDiet 5001 diet or switched to a 60% kcal TR:TREATMENT_SUMMARY fat diet (D12492, Research Diets, Inc., New Brunswick, NJ). After 8 days, mice TR:TREATMENT_SUMMARY had body weights measured then were anesthetized with isoflurane, bled TR:TREATMENT_SUMMARY retro-orbitally into K3EDTA collection tubes, euthanized by cervical TR:TREATMENT_SUMMARY dislocation, and the liver weighed and flash-frozen in liquid nitrogen #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Combine 120 mL of chilled MeOH/QC mix with 400 mL of chilled MTBE/Cholesterol SP:SAMPLEPREP_SUMMARY Ester 22:1 in a clean 500 mL stock bottle. Mix thoroughly by swirling or SP:SAMPLEPREP_SUMMARY stirring the plate and store at -20°C until use. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 6530 CH:COLUMN_NAME Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) CH:SOLVENT_A 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate CH:SOLVENT_B 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate CH:FLOW_GRADIENT 0 min 15% (B), 0–2 min 30% (B), 2–2.5 min 48% (B), 2.5–11 min 82% (B), CH:FLOW_GRADIENT 11–11.5 min 99% (B), 11.5–12 min 99% (B), 12–12.1 min 15% (B), 12.1–15 CH:FLOW_GRADIENT min 15% (B) CH:FLOW_RATE 0.6 mL/min CH:COLUMN_TEMPERATURE 65°C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Data are analyzed in a four-stage process.First, raw data are processed in an MS:MS_COMMENTS untargeted (qualitative) manner by Agilent’s software MassHunterQual to find MS:MS_COMMENTS peaks in up to 300 chromatograms. Peak features are then imported MS:MS_COMMENTS intoMassProfilerProfessional for peak alignments to seek which peaks are present MS:MS_COMMENTS in multiplechromatograms, using exclusion criteria by the minimumpercentage of MS:MS_COMMENTS chromatograms in which these peaks arepositively detected. We usually use 30% as MS:MS_COMMENTS minimumcriterion. In a tedious manual process, these peaks arethen collated and MS:MS_COMMENTS constrained into a MassHunterquantification method on the accurate mass MS:MS_COMMENTS precursorion level, using the MS/MS information and theLipidBlast library to MS:MS_COMMENTS identify lipids with manualconfirmation of adduct ions and spectral MS:MS_COMMENTS scoringaccuracy. MassHunter enables back-filling ofquantifications for peaks MS:MS_COMMENTS that were missed in theprimary peak finding process, hence yielding data MS:MS_COMMENTS setswithout missing values. The procedure is given in thepanel to the left as MS:MS_COMMENTS workflow diagram MS:MS_RESULTS_FILE ST002424_AN003947_Results.txt UNITS:Peak Height Has m/z:Yes Has RT:No RT units:No RT data #END