Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy

These files are associated with the following publication:https://doi.org/10.1210/jendso/bvaa173 And the sequence data are available at the European Nucleotide Archive: PRJEB40801 This link contains the metadata, sequences reads, and analysis files used in the study "Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy." Alpha_diversity files: File: AlphaDiversity_analysis_sham_ovex Description: R statistical analysis file for Faith's Phylogenetic Diversity (Faith's PD) and Observed Sequence Variant (SV) alpha diversity metrics File: faith_pd_sham_ovex Description: QIIME2 output file for Faith's PD alpha diversity measurements for sham/ovex samples File: obserevd_svs_sham_ovex Description: QIIME2 output file for Observed SVs alpha diversity measurements for sham/ovex samples Beta_diversity files: File: BetaDiversity_analysis_sham_ovex Description: R statistical analysis file for beta diversiy metrics File: merged.sv.sham.ovex Description: Combined SV table and taxa table for sham/ovex samples File: sv.sham.ovex Description: SV table for sham/ovex samples File: table.sham.ovex.biom Description: BIOM formated file for combined SV and taxa data. (For import into Phyloseq) File: tax.sham.ovex Description: Taxa table for sham/ovex samples File: tree.nwk Description: Phylogentic tree for sham/ovex data (For import into Phyloseq) DeSeq2 Analysis files: File: merged.sv.sham.ovex.trimmed Description: Combined SV table and taxa table for sham/ovex samples. SVs found in 4 samples or less removed. File: sv.table.sham.ovex.trimmed Description: SV table for sham/ovex samples. SVs found in 4 samples or less removed. File: sham.ovex.trimmed.biom Description: BIOM formated file for combined SV and taxa data. SVs found in 4 samples or less removed.(For import into Phyloseq) File: tax.sham.ovex.trimmed Description: Taxa table for sham/ovex samples. SVs found in 4 samples or less removed. File: tree.trimmed.nwk Description: Phylogentic tree for sham/ovex data. SVs found in 4 samples or less removed. (For import into Phyloseq) File: Phyloseq.DeSeq2.Ovex.Sham Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time points 1-5. File: Phyloseq.DeSeq2.Ovex.Sham.week3 Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 3. File: Phyloseq.DeSeq2.Ovex.Sham.week4 Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 4. File: Phyloseq.DeSeq2.Ovex.Sham.week5 Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 5. Mapping_files including metadata (for use with sequences below): File: ovex_mapping Description: Mapping file - maps barcodes to samples File: ovex_mapping_samples removed Description: Mapping file - maps barcodes to reads. Two samples removed for low sequence count. 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F 2. Plate2 C02 806rcbc121 GCA ATT AGG TAC CCG GAC TAC HVG GGT WTC TAA T 26 888 (T2) Co-Sham O File: ovex_mapping_sham_ovex_samples removed Description: Mapping file - maps barcodes to reads. Sham/ovex samples only. One sample removed for low sequence count. 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F QIIME2 Script: File: QIIME2_sham_ovex Description: This file includes the commands used in the QIIME2 pipeline.