DOI: 10.5281/zenodo.4203455
title: Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy

description: 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:<br> File: AlphaDiversity_analysis_sham_ovex<br> Description: R statistical analysis file for Faith's Phylogenetic Diversity (Faith's PD) and Observed<br> Sequence Variant (SV) alpha diversity metrics<br> File: faith_pd_sham_ovex<br> Description: QIIME2 output file for Faith's PD alpha diversity measurements for sham/ovex samples<br> File: obserevd_svs_sham_ovex<br> Description: QIIME2 output file for Observed SVs alpha diversity measurements for sham/ovex samples<br> Beta_diversity files:<br> File: BetaDiversity_analysis_sham_ovex<br> Description: R statistical analysis file for beta diversiy metrics<br> File: merged.sv.sham.ovex<br> Description: Combined SV table and taxa table for sham/ovex samples <br> File: sv.sham.ovex<br> Description: SV table for sham/ovex samples<br> File: table.sham.ovex.biom<br> Description: BIOM formated file for combined SV and taxa data. (For import into Phyloseq)<br> File: tax.sham.ovex<br> Description: Taxa table for sham/ovex samples<br> File: tree.nwk<br> Description: Phylogentic tree for sham/ovex data (For import into Phyloseq)<br> <br> DeSeq2 Analysis files:<br> File: merged.sv.sham.ovex.trimmed<br> Description: Combined SV table and taxa table for sham/ovex samples. SVs found in 4 samples or less removed. <br> File: sv.table.sham.ovex.trimmed <br> Description: SV table for sham/ovex samples. SVs found in 4 samples or less removed.<br> File: sham.ovex.trimmed.biom<br> Description: BIOM formated file for combined SV and taxa data. SVs found in 4 samples or less removed.(For import into Phyloseq)<br> File: tax.sham.ovex.trimmed<br> Description: Taxa table for sham/ovex samples. SVs found in 4 samples or less removed.<br> File: tree.trimmed.nwk<br> Description: Phylogentic tree for sham/ovex data. SVs found in 4 samples or less removed. (For import into Phyloseq)<br> File: Phyloseq.DeSeq2.Ovex.Sham<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time points 1-5.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week3<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 3.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week4<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 4.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week5<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 5.<br> <br> <br> Mapping_files including metadata (for use with sequences below):<br> File: ovex_mapping <br> Description: Mapping file - maps barcodes to samples<br> File: ovex_mapping_samples removed<br> Description: Mapping file - maps barcodes to reads. Two samples removed for low sequence count.<br> 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F<br> 2. Plate2 C02 806rcbc121 GCA ATT AGG TAC CCG GAC TAC HVG GGT WTC TAA T 26 888 (T2) Co-Sham O<br> File: ovex_mapping_sham_ovex_samples removed<br> Description: Mapping file - maps barcodes to reads. Sham/ovex samples only. One sample removed for low sequence count.<br> 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F<br> QIIME2 Script: File: QIIME2_sham_ovex<br> Description: This file includes the commands used in the QIIME2 pipeline.