Skeletal muscle metabolomics and lipidomics, and whole-animal indirect calorimetry data from breast cancer patient-derived xenograft implanted mice.

Study DescriptionFemale 8 week old NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were implanted with a HER2/neu+ overexpressing patient-derived xenograft (PDX) in the mammary fat pads. Mice were treated with pioglitazone or vehicle for 4 weeks and then collected.Metabolomics/Lipidomics dataThere are two folders, Untargeted_Metabolomics and Quantitative_Lipidomics. Each folder contains a sub folder with the raw .mzml files and an .xlsx files with the identified compounds.Whole-animal indirect calorimetryOne folder contains the raw indirect calorimetry files named Indirect_Calorimetry. Files are named by group, either as Pioglitazone_#.csv or Vehicle_#.csv.Supplementary DataAll additional supplementary data is described below.Supplementary Data 1. Untargeted metabolomics internal standard stability in QC samples.Supplementary Data 2. Cumulative mouse body weights in grams.Supplementary Data 3. Unnormalized gene expression counts for Pioglitazone and Vehicle groups.Supplementary Data 4. K-means cluster-5 gene list.Supplementary Data 5. Pioglitazone- vs. vehicle-treated all adjusted p-value significant pathways from GO Biological.Supplementary Data 6. Pioglitazone- vs. vehicle-treated all adjusted p-value significant pathways from GO Cellular.Supplementary Data 7. Pioglitazone- vs. vehicle-treated all adjusted p-value significant pathways from GO Molecular.Supplementary Data 8. Pioglitazone- vs. vehicle-treated all adjusted p-value significant pathways from KEGG.Supplementary Data 9. Pioglitazone- vs. vehicle-treated all adjusted p-value significant pathways from Reactome.Directory Tree.├── Indirect_Calorimetry│ ├── Pioglitazone_1.csv│ ├── Pioglitazone_2.csv│ ├── Pioglitazone_3.csv│ ├── Pioglitazone_4.csv│ ├── Pioglitazone_5.csv│ ├── Vehicle_1.csv│ ├── Vehicle_2.csv│ ├── Vehicle_3.csv│ └── Vehicle_4.csv├── Quantitative_Lipidomics│ ├── Lipidomics_mzml│ │ ├── CON-1_N.mzML│ │ ├── CON-1_P.mzML│ │ ├── CON-2_N.mzML│ │ ├── CON-2_P.mzML│ │ ├── CON-3_N.mzML│ │ ├── CON-3_P.mzML│ │ ├── CON-4_N.mzML│ │ ├── CON-4_P.mzML│ │ ├── PIO-1_N.mzML│ │ ├── PIO-1_P.mzML│ │ ├── PIO-2_N.mzML│ │ ├── PIO-2_P.mzML│ │ ├── PIO-3_N.mzML│ │ ├── PIO-3_P.mzML│ │ ├── PIO-4_N.mzML│ │ ├── PIO-4_P.mzML│ │ ├── PIO-5_N.mzML│ │ ├── PIO-5_P.mzML│ │ ├── PIO-6_N.mzML│ │ ├── PIO-6_P.mzML│ │ ├── VEH-1_N.mzML│ │ ├── VEH-1_P.mzML│ │ ├── VEH-2_N.mzML│ │ ├── VEH-2_P.mzML│ │ ├── VEH-3_N.mzML│ │ ├── VEH-3_P.mzML│ │ ├── VEH-4_N.mzML│ │ ├── VEH-4_P.mzML│ │ ├── VEH-5_N.mzML│ │ └── VEH-5_P.mzML│ └── Quantitative_Lipidomics_All_Identified_Lipids.xlsx├── Supplementary_Tables_and_Figures.pdf├── SupplementaryData1_Stability_of_Internal_Standards_in_QC_Samples.xlsx├── SupplementaryData2_Animal_Body_Weights.xlsx├── SupplementaryData3_Unnormalized_gene_expression_counts_for_Pioglitazone_and_Vehicle.tsv├── SupplementaryData4_RNAseq_k_means_cluster5_enrichment.xlsx├── SupplementaryData5_GO_Biological_Pathways_Pioglitazone_vs_Vehicle_all_Adj.p_significant.xlsx├── SupplementaryData6_GO_Cellular_Pathways_Pioglitazone_vs_Vehicle_all_Adj.p_significant.xlsx├── SupplementaryData7_GO_Molecular_Pathways_Pioglitazone_vs_Vehicle_all_Adj.p_significant.xlsx├── SupplementaryData8_KEGG_Pathways_Pioglitazone_vs_Vehicle_all_Adj.p_significant.xlsx├── SupplementaryData9_Curated_Reactome_Pathways_Pioglitazone_vs_Vehicle_all_Adj.p_significant.xlsx└── Untargeted_Metabolomics ├── Metabolomics_mzml │ ├── CON-1_N.mzML │ ├── CON-1_P.mzML │ ├── CON-2_N.mzML │ ├── CON-2_P.mzML │ ├── CON-3_N.mzML │ ├── CON-3_P.mzML │ ├── CON-4_N.mzML │ ├── CON-4_P.mzML │ ├── PIO-1_N.mzML │ ├── PIO-1_P.mzML │ ├── PIO-2_N.mzML │ ├── PIO-2_P.mzML │ ├── PIO-3_N.mzML │ ├── PIO-3_P.mzML │ ├── PIO-4_N.mzML │ ├── PIO-4_P.mzML │ ├── PIO-5_N.mzML │ ├── PIO-5_P.mzML │ ├── PIO-6_N.mzML │ ├── PIO-6_P.mzML │ ├── VEH-1_N.mzML │ ├── VEH-1_P.mzML │ ├── VEH-2_N.mzML │ ├── VEH-2_P.mzML │ ├── VEH-3_N.mzML │ ├── VEH-3_P.mzML │ ├── VEH-4_N.mzML │ ├── VEH-4_P.mzML │ ├── VEH-5_N.mzML │ └── VEH-5_P.mzML └── Untargeted_Metabolomics_All_Detected_Metabolites.xlsx