Multi-omic dissection of reversible and persistent molecular alterations in diet-induced obesity - Replication Data

Raw and input data to replicate the results in the paper: Multi-omic dissection of reversible and persistent molecular alterations in diet-induced obesity. DOI: https://doi.org/10.64898/2026.09.08.749914. Contains: Inputs: folder necessary to replicate the results jointly with the scripts available in https://github.com/jordirofes/gnotobiomics_project_data_analysis github repository. The folder must be decompressed and must be located in the same folder as the scripts folder. The contents of the inputs folder are: Mice metadata files Untargeted metabolomics: hermes, mummichog and xcms results To fully replicate the pre-processing, remove the input files and decompress the Untargeted_Metabolomics.rar inside the Untargeted_Metabolomics input folder. Epigenomics: methrix files To fully replicate the pre-processing, remove the two .rds files within the WGB_DNA_Methylation folder (keep the Lima and GFCV folders intact). RNA Sequencing: processed matrix and other required files Metallomics: processed matrix Metagenomics: processed matrixes and other required files (functional and taxonomy) Targeted metabolomics: processed files Histone proteomics: processed files Metallomics_Raw_ICP_Files_LiMa_GFCV.rar Metallomics raw ICP-MS files Targeted_Metabolomics_Raw_LiMa_GFCV.rar Targeted Metabolomics raw files Targeted_Metabolomics_SCFA_Raw_LiMa_GFCV.rar Targeted Metabolomics Short Chain Fatty Acids (SCFA) raw file Untargeted_Metabolomics_mzML.rar. Untargeted mzML files Supplementary_Files: supplementary .xlsx files from the article Supplementary files with Shotgun_Metagenomics data include the old taxons updated in Supplementary Tables 3 and 5 and the list of changes.