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

<p>These files are associated with the following publication:<a href="https://doi.org/10.1210/jendso/bvaa173">https://doi.org/10.1210/jendso/bvaa173</a></p> <p>And the sequence data are available at the European Nucleotide Archive: PRJEB40801</p> <p>This link contains the metadata, sequences reads, and analysis files used in the study &quot;Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy.&quot;</p> <p>Alpha_diversity files:<br> &nbsp;&nbsp; &nbsp;File: AlphaDiversity_analysis_sham_ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: R statistical analysis file for Faith&#39;s Phylogenetic Diversity (Faith&#39;s PD) and Observed<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; Sequence Variant (SV) alpha diversity metrics<br> &nbsp;&nbsp; &nbsp;File: faith_pd_sham_ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: QIIME2 output file for Faith&#39;s PD alpha diversity measurements for sham/ovex samples<br> &nbsp;&nbsp; &nbsp;File: obserevd_svs_sham_ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: QIIME2 output file for Observed SVs alpha diversity measurements for sham/ovex samples<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;</p> <p>Beta_diversity files:<br> &nbsp;&nbsp; &nbsp;File: BetaDiversity_analysis_sham_ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: R statistical analysis file for beta diversiy metrics<br> &nbsp;&nbsp; &nbsp;File: merged.sv.sham.ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Combined SV table and taxa table for sham/ovex samples &nbsp;<br> &nbsp;&nbsp; &nbsp;File: sv.sham.ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: SV table for sham/ovex samples<br> &nbsp;&nbsp; &nbsp;File: table.sham.ovex.biom<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: BIOM formated file for combined SV and taxa data. (For import into Phyloseq)<br> &nbsp;&nbsp; &nbsp;File: tax.sham.ovex<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Taxa table for sham/ovex samples<br> &nbsp;&nbsp; &nbsp;File: tree.nwk<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Phylogentic tree for sham/ovex data (For import into Phyloseq)<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;<br> DeSeq2 Analysis files:<br> &nbsp;&nbsp; &nbsp;File: merged.sv.sham.ovex.trimmed<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Combined SV table and taxa table for sham/ovex samples. SVs found in 4 samples or less removed. &nbsp;<br> &nbsp;&nbsp; &nbsp;File: sv.table.sham.ovex.trimmed &nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: SV table for sham/ovex samples. SVs found in 4 samples or less removed.<br> &nbsp;&nbsp; &nbsp;File: sham.ovex.trimmed.biom<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: BIOM formated file for combined SV and taxa data. SVs found in 4 samples or less removed.(For import into Phyloseq)<br> &nbsp;&nbsp; &nbsp;File: tax.sham.ovex.trimmed<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Taxa table for sham/ovex samples. SVs found in 4 samples or less removed.<br> &nbsp;&nbsp; &nbsp;File: tree.trimmed.nwk<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Phylogentic tree for sham/ovex data. SVs found in 4 samples or less removed. (For import into Phyloseq)<br> &nbsp;&nbsp; &nbsp;File: Phyloseq.DeSeq2.Ovex.Sham<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time points 1-5.<br> &nbsp;&nbsp; &nbsp;File: Phyloseq.DeSeq2.Ovex.Sham.week3<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 3.<br> &nbsp;&nbsp;&nbsp; File: Phyloseq.DeSeq2.Ovex.Sham.week4<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 4.<br> &nbsp;&nbsp; &nbsp;File: Phyloseq.DeSeq2.Ovex.Sham.week5<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 5.<br> &nbsp;&nbsp; &nbsp;<br> &nbsp;&nbsp; &nbsp;<br> Mapping_files including metadata (for use with sequences below):<br> &nbsp;&nbsp; &nbsp;File: ovex_mapping &nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Mapping file - maps barcodes to samples<br> &nbsp;&nbsp; &nbsp;File: ovex_mapping_samples removed<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Mapping file - maps barcodes to reads. Two samples removed for low sequence count.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1. Plate2&nbsp;&nbsp; &nbsp;A08&nbsp;&nbsp; &nbsp;806rcbc103&nbsp;&nbsp; &nbsp;GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T&nbsp;&nbsp; &nbsp;8&nbsp;&nbsp; &nbsp;870 (T2)&nbsp;&nbsp; &nbsp;Ovex&nbsp;&nbsp; &nbsp;F<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;2. Plate2&nbsp;&nbsp; &nbsp;C02&nbsp;&nbsp; &nbsp;806rcbc121&nbsp;&nbsp; &nbsp;GCA ATT AGG TAC CCG GAC TAC HVG GGT WTC TAA T&nbsp;&nbsp; &nbsp;26&nbsp;&nbsp; &nbsp;888 (T2)&nbsp;&nbsp; &nbsp;Co-Sham&nbsp;&nbsp; &nbsp;O<br> &nbsp;&nbsp; &nbsp;File: ovex_mapping_sham_ovex_samples removed<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;Description: Mapping file - maps barcodes to reads. Sham/ovex samples only. One sample removed for low sequence count.<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;1. Plate2&nbsp;&nbsp; &nbsp;A08&nbsp;&nbsp; &nbsp;806rcbc103&nbsp;&nbsp; &nbsp;GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T&nbsp;&nbsp; &nbsp;8&nbsp;&nbsp; &nbsp;870 (T2)&nbsp;&nbsp; &nbsp;Ovex&nbsp;&nbsp; &nbsp;F<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;</p> <p>QIIME2 Script:</p> <p>File: QIIME2_sham_ovex<br> &nbsp;&nbsp; &nbsp;Description: This file includes the commands used in the QIIME2 pipeline.</p>